├── .gitattributes ├── README.md ├── ascii2num ├── bam2fasta.pl ├── calc_pop_divs.pl ├── calc_vcf_diversity.pl ├── convert_fastq_quality.pl ├── convert_trf.pl ├── count_vcf_pairs.pl ├── detect_mutations.pl ├── downsample_vcf.pl ├── extract_bam_pairs.pl ├── extract_split_seqs.pl ├── fasta_process.pl ├── gff2fasta.pl ├── gff2tables.pl ├── ggplot-liner-fit.R ├── ggplot-windows-count.R ├── ggplot-windows-multi.R ├── intervals2bed ├── map_pos2intervals.pl ├── map_records.pl ├── maskedSEQ2bed.pl ├── paintGenomeBlocks.pl ├── parallel_baseml.pl ├── parallel_codeml.pl ├── parseSEQs.pl ├── plot-scatter_with_lines.R ├── reference_align.pl ├── rename_fasta.pl ├── sam2fastq.pl ├── site_perl └── MyPerl │ ├── Align.pm │ ├── Compare.pm │ ├── Convert.pm │ ├── FileIO.pm │ ├── README.md │ ├── Statistics.pm │ └── Vcf.pm ├── subtotal_stats.pl ├── vcf2tables.pl └── vcf_process.pl /.gitattributes: -------------------------------------------------------------------------------- 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