├── BABAPPA └── good clipgard │ ├── QCseq │ └── ATCOL.fasta_QC.fasta.log.txt │ ├── analysis │ ├── codemloutput │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155 │ │ │ ├── M0 │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── treefile.treefile │ │ │ │ ├── 2NG.dN │ │ │ │ ├── 2NG.dS │ │ │ │ ├── 2NG.t │ │ │ │ └── 4fold.nuc │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.dN │ │ │ │ ├── 2NG.dS │ │ │ │ └── 2NG.t │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.t │ │ │ │ ├── 2NG.dN │ │ │ │ └── 2NG.dS │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.dN │ │ │ │ ├── 2NG.dS │ │ │ │ └── 2NG.t │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.t │ │ │ │ ├── 2NG.dN │ │ │ │ └── 2NG.dS │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.dN │ │ │ │ ├── 2NG.dS │ │ │ │ └── 2NG.t │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.t │ │ │ │ ├── 2NG.dN │ │ │ │ └── 2NG.dS │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.dN │ │ │ │ ├── 2NG.dS │ │ │ │ └── 2NG.t │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.t │ │ │ │ ├── 2NG.dN │ │ │ │ └── 2NG.dS │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.dN │ │ │ │ ├── 2NG.dS │ │ │ │ └── 2NG.t │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.t │ │ │ │ ├── 2NG.dN │ │ │ │ └── 2NG.dS │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.dN │ │ │ │ ├── 2NG.dS │ │ │ │ └── 2NG.t │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.t │ │ │ │ ├── 2NG.dN │ │ │ │ └── 2NG.dS │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.dN │ │ │ │ ├── 2NG.dS │ │ │ │ └── 2NG.t │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ ├── 2NG.t │ │ │ │ ├── 2NG.dN │ │ │ │ └── 2NG.dS │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ └── 2NG.t │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ └── 2NG.t │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ └── 2NG.t │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ └── 2NG.t │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ └── 2NG.t │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ └── 2NG.t │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ ├── rst1 │ │ │ │ └── 2NG.t │ │ │ ├── treefile.treefile │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11.treefile │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11.treefile │ │ │ └── AT2G47890_AT2G47890.1_Athaliana_Araport11.treefile │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456 │ │ │ ├── M0 │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── treefile.treefile │ │ │ ├── 2NG.t │ │ │ ├── 2NG.dN │ │ │ └── 2NG.dS │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ └── 2NG.t │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ └── 2NG.t │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ └── 2NG.t │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ └── 2NG.t │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ └── 2NG.t │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ └── 2NG.t │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ └── 2NG.t │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ └── 2NG.t │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ └── 2NG.t │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── treefile.treefile │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11.treefile │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11.treefile │ │ │ └── AT2G47890_AT2G47890.1_Athaliana_Araport11.treefile │ ├── codemloutput - Copy │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155 │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_B │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_BS │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_BS_NULL │ │ │ │ ├── rub │ │ │ │ └── rst1 │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11.treefile │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11.treefile │ │ │ └── AT2G47890_AT2G47890.1_Athaliana_Araport11.treefile │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456 │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_B │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_BS │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT2G47890_AT2G47890.1_Athaliana_Araport11_BS_NULL │ │ │ ├── rub │ │ │ ├── rst1 │ │ │ └── 4fold.nuc │ │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11.treefile │ │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11.treefile │ │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile │ │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11.treefile │ │ │ └── AT2G47890_AT2G47890.1_Athaliana_Araport11.treefile │ ├── BHanalysis │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155 │ │ │ └── LRT_results_lnL_np_values.xlsx │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456 │ │ │ └── LRT_results_lnL_np_values.xlsx │ ├── sitemodelanalysis │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155 │ │ │ └── lnL_np_values.csv │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456 │ │ │ └── lnL_np_values.csv │ ├── BHanalysis4sitemodel │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456 │ │ │ └── lrt_results.csv │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155 │ │ │ └── lrt_results.csv │ ├── sitemodel │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155 │ │ │ ├── rub │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ ├── 2NG.t │ │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.treefile │ │ │ └── 4fold.nuc │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456 │ │ │ ├── rub │ │ │ ├── 4fold.nuc │ │ │ ├── 2NG.dN │ │ │ ├── 2NG.dS │ │ │ ├── 2NG.t │ │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.treefile │ ├── treefiles │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.treefile │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.treefile │ └── foregroundbranch │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155 │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11.treefile │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11.treefile │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11.treefile │ │ └── AT2G47890_AT2G47890.1_Athaliana_Araport11.treefile │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456 │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11.treefile │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11.treefile │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11.treefile │ │ └── AT2G47890_AT2G47890.1_Athaliana_Araport11.treefile │ ├── iqtreeoutput │ └── ATCOL │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155 │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.ckp.gz │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.model.gz │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.bionj │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.parstree │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.contree │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.treefile │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456 │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.ckp.gz │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.model.gz │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.bionj │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.parstree │ │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.contree │ │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.treefile │ ├── treefiles │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.treefile │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.treefile │ ├── foregroundbranch │ ├── ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155 │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11.treefile │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11.treefile │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11.treefile │ │ └── AT2G47890_AT2G47890.1_Athaliana_Araport11.treefile │ └── ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456 │ │ ├── AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile │ │ ├── AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile │ │ ├── AT1G68520_AT1G68520.1_Athaliana_Araport11.treefile │ │ ├── AT1G73870_AT1G73870.1_Athaliana_Araport11.treefile │ │ ├── AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile │ │ ├── AT2G33500_AT2G33500.1_Athaliana_Araport11.treefile │ │ └── AT2G47890_AT2G47890.1_Athaliana_Araport11.treefile │ └── recombination_blocks │ └── ATCOL │ └── split_recombination_blocks.log └── BABAPPA_GUI ├── butterfly_icon.ico ├── butterfly_icon.png └── babappa_project └── __pycache__ └── babappa_api.cpython-310.pyc /BABAPPA/good clipgard/QCseq/ATCOL.fasta_QC.fasta.log.txt: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/M0/rub: -------------------------------------------------------------------------------- 1 | 2 | 3 | TREE # 1 4 | -------------------------------------------------------------------------------- /BABAPPA/good 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AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/iqtreeoutput/ATCOL/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.parstree: -------------------------------------------------------------------------------- 1 | (AT1G25440_AT1G25440.1_Athaliana_Araport11:0.1747499050,AT1G68520_AT1G68520.1_Athaliana_Araport11:0.2717167559,(AT2G24790_AT2G24790.1_Athaliana_Araport11:0.4658532721,((AT1G73870_AT1G73870.1_Athaliana_Araport11:0.0994553635,(AT1G28050_AT1G28050.1_Athaliana_Araport11:0.2717167559,AT2G33500_AT2G33500.1_Athaliana_Araport11:0.1747499050):0.2022297122):0.3381014304,AT2G47890_AT2G47890.1_Athaliana_Araport11:0.4658532721):0.2510460251):0.2612955906); 2 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/treefile.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); 2 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/iqtreeoutput/ATCOL/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.parstree: -------------------------------------------------------------------------------- 1 | ((AT1G68520_AT1G68520.1_Athaliana_Araport11:0.3102920825,AT1G25440_AT1G25440.1_Athaliana_Araport11:0.3277720360):0.1191954308,AT1G73870_AT1G73870.1_Athaliana_Araport11:0.9699769053,(AT2G24790_AT2G24790.1_Athaliana_Araport11:0.1361573374,(AT2G47890_AT2G47890.1_Athaliana_Araport11:0.2988953866,(AT1G28050_AT1G28050.1_Athaliana_Araport11:0.1536491677,AT2G33500_AT2G33500.1_Athaliana_Araport11:0.1448354720):0.1762977473):0.1191954308):0.1448354720); 2 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/M0/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/M0/treefile.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); 2 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/sitemodel/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/sitemodel/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/sitemodel/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/sitemodel/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/sitemodel/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/sitemodel/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/iqtreeoutput/ATCOL/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.contree: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:0.0000026217,AT1G28050_AT1G28050.1_Athaliana_Araport11:0.4367011743,(AT2G47890_AT2G47890.1_Athaliana_Araport11:3.8872826881,((AT1G73870_AT1G73870.1_Athaliana_Araport11:2.2079288802,AT2G24790_AT2G24790.1_Athaliana_Araport11:2.3952613274)87:0.6299768213,(AT1G68520_AT1G68520.1_Athaliana_Araport11:0.0772039381,AT1G25440_AT1G25440.1_Athaliana_Araport11:0.3525182752)67:0.0000026217)99:3.0169961008)76:4.5679849020); 2 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/M0/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/M0/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/M0/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/M0/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/iqtreeoutput/ATCOL/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.contree: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.5067820709,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.7568134358,(AT2G47890_AT2G47890.1_Athaliana_Araport11:9.9999987564,((AT1G73870_AT1G73870.1_Athaliana_Araport11:9.9999988320,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.6715870869,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9205454335)100:8.8728780106)100:9.9999986878,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.9999984852)100:9.9999986197)100:9.9999985001); 2 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/M0/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/M0/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/foregroundbranch/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:0.3113022419,AT1G28050_AT1G28050.1_Athaliana_Araport11:3.1754259572,(AT2G47890_AT2G47890.1_Athaliana_Araport11:60.6175418747,((AT1G73870_AT1G73870.1_Athaliana_Araport11:7.4283772659,AT2G24790_AT2G24790.1_Athaliana_Araport11:61.6361514742)90.9/87:7.0963679350,(AT1G68520_AT1G68520.1_Athaliana_Araport11:0.8693789650,AT1G25440_AT1G25440.1_Athaliana_Araport11#1:2.6291073705)93.7/67:9.4910965120)99.9/99:9.4759942590)96.1/76:24.2124509800); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/foregroundbranch/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:0.3113022419,AT1G28050_AT1G28050.1_Athaliana_Araport11#1:3.1754259572,(AT2G47890_AT2G47890.1_Athaliana_Araport11:60.6175418747,((AT1G73870_AT1G73870.1_Athaliana_Araport11:7.4283772659,AT2G24790_AT2G24790.1_Athaliana_Araport11:61.6361514742)90.9/87:7.0963679350,(AT1G68520_AT1G68520.1_Athaliana_Araport11:0.8693789650,AT1G25440_AT1G25440.1_Athaliana_Araport11:2.6291073705)93.7/67:9.4910965120)99.9/99:9.4759942590)96.1/76:24.2124509800); -------------------------------------------------------------------------------- /BABAPPA/good 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(AT2G33500_AT2G33500.1_Athaliana_Araport11:0.3113022419,AT1G28050_AT1G28050.1_Athaliana_Araport11:3.1754259572,(AT2G47890_AT2G47890.1_Athaliana_Araport11:60.6175418747,((AT1G73870_AT1G73870.1_Athaliana_Araport11#1:7.4283772659,AT2G24790_AT2G24790.1_Athaliana_Araport11:61.6361514742)90.9/87:7.0963679350,(AT1G68520_AT1G68520.1_Athaliana_Araport11:0.8693789650,AT1G25440_AT1G25440.1_Athaliana_Araport11:2.6291073705)93.7/67:9.4910965120)99.9/99:9.4759942590)96.1/76:24.2124509800); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/foregroundbranch/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | 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(AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11#1:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/sitemodel/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 6 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | GCGTGG 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | GCGGGT 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | TTCCCA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TCTATA 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | ATCTAA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | ACTTAG 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | AAGCTA 23 | 24 | 25 | codons included 26 | 26 32 35 37 48 120 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11#1:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11#1:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11#1:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11#1:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11#1:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G33500_AT2G33500.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11#1:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G47890_AT2G47890.1_Athaliana_Araport11.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11#1:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/M0/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 6 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | GCGTGG 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | GCGGGT 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | TTCCCA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TCTATA 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | ATCTAA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | ACTTAG 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | AAGCTA 23 | 24 | 25 | codons included 26 | 26 32 35 37 48 120 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/sitemodel/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); 2 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/iqtreeoutput/ATCOL/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.treefile: -------------------------------------------------------------------------------- 1 | (AT2G33500_AT2G33500.1_Athaliana_Araport11:2.6070922038,AT1G28050_AT1G28050.1_Athaliana_Araport11:4.8754827669,(AT2G47890_AT2G47890.1_Athaliana_Araport11:10.4960233510,((AT1G73870_AT1G73870.1_Athaliana_Araport11:13.1941094123,(AT1G68520_AT1G68520.1_Athaliana_Araport11:7.8636626347,AT1G25440_AT1G25440.1_Athaliana_Araport11:3.9747272536)97.4/100:6.9115119610)97.8/100:13.1941094000,AT2G24790_AT2G24790.1_Athaliana_Araport11:9.5829065142)98.7/100:16.7936551800)99.8/100:10.4960233600); 2 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/recombination_blocks/ATCOL/split_recombination_blocks.log: -------------------------------------------------------------------------------- 1 | Input FASTA: msa/ATCOL.fasta_QC_msa.best.fas 2 | GARD JSON: gard_output/ATCOL.fasta_QC_msa.best.gard.json 3 | Alignment length: 1368 nt 4 | Scale factor: 3 5 | 6 | Blocks (codon): ['1-155', '156-456'] 7 | Blocks (nt): ['1-465', '466-1368'] 8 | 9 | ✔ Saved block 1: recombination_blocks/ATCOL/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155.fas 10 | Trimmed 0 nt at start, 0 nt at end 11 | 12 | ✔ Saved block 2: recombination_blocks/ATCOL/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456.fas 13 | Trimmed 0 nt at start, 0 nt at end 14 | 15 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G33500_AT2G33500.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G33500_AT2G33500.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G47890_AT2G47890.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G47890_AT2G47890.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G33500_AT2G33500.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G33500_AT2G33500.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G47890_AT2G47890.1_Athaliana_Araport11_B/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G47890_AT2G47890.1_Athaliana_Araport11_BS/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G25440_AT1G25440.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G25440_AT1G25440.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G25440_AT1G25440.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G28050_AT1G28050.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G28050_AT1G28050.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G28050_AT1G28050.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G68520_AT1G68520.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G68520_AT1G68520.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G68520_AT1G68520.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G73870_AT1G73870.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G73870_AT1G73870.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G73870_AT1G73870.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G24790_AT2G24790.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G24790_AT2G24790.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G24790_AT2G24790.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G24790_AT2G24790.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G33500_AT2G33500.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G33500_AT2G33500.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G33500_AT2G33500.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G33500_AT2G33500.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G47890_AT2G47890.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G47890_AT2G47890.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G47890_AT2G47890.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G47890_AT2G47890.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G33500_AT2G33500.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G47890_AT2G47890.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G33500_AT2G33500.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput - Copy/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G47890_AT2G47890.1_Athaliana_Araport11_BS_NULL/4fold.nuc: -------------------------------------------------------------------------------- 1 | 7 2 2 | 3 | AT2G33500_AT2G33500.1_Athaliana_Araport11 4 | CC 5 | 6 | AT1G28050_AT1G28050.1_Athaliana_Araport11 7 | TC 8 | 9 | AT2G47890_AT2G47890.1_Athaliana_Araport11 10 | AA 11 | 12 | AT1G73870_AT1G73870.1_Athaliana_Araport11 13 | TT 14 | 15 | AT1G68520_AT1G68520.1_Athaliana_Araport11 16 | AA 17 | 18 | AT1G25440_AT1G25440.1_Athaliana_Araport11 19 | AA 20 | 21 | AT2G24790_AT2G24790.1_Athaliana_Araport11 22 | TA 23 | 24 | 25 | codons included 26 | 281 289 27 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS_NULL/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS_NULL/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS_NULL/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS_NULL/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G24790_AT2G24790.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G24790_AT2G24790.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G24790_AT2G24790.1_Athaliana_Araport11_BS_NULL/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G33500_AT2G33500.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G33500_AT2G33500.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G33500_AT2G33500.1_Athaliana_Araport11_BS_NULL/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G47890_AT2G47890.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1125 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5021 0.5519 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6187 0.6584 0.8042 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.4997 0.5921 0.6054 0.3365 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.5452 0.6213 0.6652 0.3476 0.1075 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6938 0.7254 0.6628 0.4347 0.5078 0.5242 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G47890_AT2G47890.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.7971 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.0000 3.0000 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0000 3.0000 2.7353 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 1.7064 3.9522 3.0000 3.0000 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 3.0000 3.0000 3.0000 0.7996 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.0000 3.0000 1.8451 1.6580 1.8227 2.4095 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block1_1-155/AT2G47890_AT2G47890.1_Athaliana_Araport11_BS_NULL/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8193 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 3.2703 3.3598 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.4930 3.5438 3.6863 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 2.3625 4.1182 3.4757 2.9180 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.3782 3.5084 3.6006 2.9395 0.8190 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 3.7429 3.8086 2.8276 2.1932 2.4894 2.9528 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G25440_AT1G25440.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G28050_AT1G28050.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G68520_AT1G68520.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT1G73870_AT1G73870.1_Athaliana_Araport11_BS/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11_B/2NG.dN: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.1827 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 0.5007 0.5645 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 0.6495 0.7183 0.6948 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 0.7243 0.8111 0.7387 0.5470 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 0.7568 0.8784 0.7681 0.4926 0.2492 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 0.6370 0.7309 0.5790 0.5624 0.5167 0.5326 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11_B/2NG.dS: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.6646 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.2007 2.4135 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.0261 3.9310 3.0000 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.0000 2.6471 1.8266 2.0164 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.0000 2.2078 2.5799 1.9085 1.0240 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 1.6287 1.6166 2.2462 1.3540 2.6681 1.7121 9 | -------------------------------------------------------------------------------- /BABAPPA/good clipgard/analysis/codemloutput/ATCOL.fasta_QC_msa.best.fas.gard_block2_156-456/AT2G24790_AT2G24790.1_Athaliana_Araport11_B/2NG.t: -------------------------------------------------------------------------------- 1 | 7 2 | AT2G33500_AT2G33500.1_Athaliana_Araport11 3 | AT1G28050_AT1G28050.1_Athaliana_Araport11 0.8747 4 | AT2G47890_AT2G47890.1_Athaliana_Araport11 2.6620 2.9748 5 | AT1G73870_AT1G73870.1_Athaliana_Araport11 3.5753 4.4186 3.6646 6 | AT1G68520_AT1G68520.1_Athaliana_Araport11 3.6416 3.6357 2.9146 2.6011 7 | AT1G25440_AT1G25440.1_Athaliana_Araport11 3.7155 3.5161 3.4712 2.4017 1.2447 8 | AT2G24790_AT2G24790.1_Athaliana_Araport11 2.5929 2.8031 2.8829 2.2443 2.9885 2.3951 9 | --------------------------------------------------------------------------------