├── .github └── workflows │ └── main.yml ├── .gitignore ├── .readthedocs.yaml ├── BIORXIV-2020-291484v1-Brown.pdf ├── CIAlign ├── CIAlign ├── CIAlign.py ├── __init__.py ├── _version.py ├── argP.py ├── consensusSeq.py ├── cropDiv.py ├── cropSeq.py ├── insertions.py ├── matrices.py ├── matrices.txt ├── miniAlignments.py ├── palettes.py ├── parsingFunctions.py ├── ranges.txt ├── runCIAlign.py ├── similarityMatrix.py ├── similarity_matrices │ ├── BLOSUM100 │ ├── BLOSUM30 │ ├── BLOSUM35 │ ├── BLOSUM40 │ ├── BLOSUM45 │ ├── BLOSUM50 │ ├── BLOSUM55 │ ├── BLOSUM60 │ ├── BLOSUM62 │ ├── BLOSUM65 │ ├── BLOSUM70 │ ├── BLOSUM75 │ ├── BLOSUM80 │ ├── BLOSUM85 │ ├── BLOSUM90 │ ├── BLOSUMN │ ├── DAYHOFF │ ├── GONNET │ ├── IDENTITY │ ├── MATCH │ ├── NUC.4.2 │ ├── NUC.4.4 │ ├── PAM10 │ ├── PAM100 │ ├── PAM110 │ ├── PAM120 │ ├── PAM130 │ ├── PAM140 │ ├── PAM150 │ ├── PAM160 │ ├── PAM170 │ ├── PAM180 │ ├── PAM190 │ ├── PAM20 │ ├── PAM200 │ ├── PAM210 │ ├── PAM220 │ ├── PAM230 │ ├── PAM240 │ ├── PAM250 │ ├── PAM260 │ ├── PAM270 │ ├── PAM280 │ ├── PAM290 │ ├── PAM30 │ ├── PAM300 │ ├── PAM310 │ ├── PAM320 │ ├── PAM330 │ ├── PAM340 │ ├── PAM350 │ ├── PAM360 │ ├── PAM370 │ ├── PAM380 │ ├── PAM390 │ ├── PAM40 │ ├── PAM400 │ ├── PAM410 │ ├── PAM420 │ ├── PAM430 │ ├── PAM440 │ ├── PAM450 │ ├── PAM460 │ ├── PAM470 │ ├── PAM480 │ ├── PAM490 │ ├── PAM50 │ ├── PAM500 │ ├── PAM60 │ ├── PAM70 │ ├── PAM80 │ └── PAM90 └── utilityFunctions.py ├── CIAlign_poster.pdf ├── LICENSE ├── MANIFEST.in ├── README.md ├── benchmarking ├── BAliBase │ ├── highly_stringent_config_BB.ini │ ├── low_stringent_config_BB.ini │ ├── med_stringent_config_BB.ini │ ├── run_alignment.sh │ └── run_cialign.sh ├── BadRead │ ├── dwv.fasta │ ├── med_stringent_config_BadRead.ini │ ├── run_alignment.sh │ ├── run_all.sh │ ├── run_cialign.sh │ ├── run_cialign_cons.sh │ └── run_simulations.sh ├── EvolvAGene │ ├── highly_stringent_config_EvolvAGene.ini │ ├── human_gapdh.fasta │ ├── human_gapdh.txt │ ├── human_gapdh_prot.fasta │ ├── low_stringent_config_EvolvAGene.ini │ ├── make_cons.sh │ ├── med_stringent_config_EvolvAGene.ini │ ├── run_alignment.sh │ ├── run_all.sh │ ├── run_cialign.sh │ ├── run_simluation.sh │ └── run_trees.sh ├── INDELible │ ├── control_nucleotide.txt │ ├── highly_stringent_config_INDELible.ini │ ├── indelible_guide_tree.nwk │ ├── low_stringent_config_INDELible.ini │ ├── med_stringent_config_INDELible.ini │ ├── run_alignment.sh │ ├── run_all.sh │ ├── run_cialign.sh │ ├── run_simulations.sh │ └── run_trees.sh ├── Online_Figures │ ├── 1-A1.png │ ├── 1-A2.png │ ├── 1-B1.png │ ├── 1-B2.png │ ├── 1-C1.png │ ├── 1-C2.png │ ├── 1-D1.png │ ├── 1-D2.png │ └── README.md ├── QuanTest2 │ ├── adjust_msa_to_quantest2.py │ ├── quantest2.py │ ├── quantest2_cialign.py │ └── quantest2_cialign.sh ├── functions │ ├── AlignmentStats.py │ └── convertLog.py ├── tables │ ├── OT_1_Alignment_Statistics.tsv │ ├── OT_2_BadRead.tsv │ ├── OT_3_HomFam.tsv │ ├── OT_4_QuanTest2.tsv │ ├── OT_5_All_Aligners.tsv │ ├── OT_6_Trimmers.tsv │ ├── OT_7_Realignment.tsv │ ├── OT_8_Pfam.tsv │ ├── OT_9_1000_genomes.tsv │ └── README.md └── time_and_memory │ ├── README.md │ ├── const_size_diff_gap.tsv │ ├── crop_ends.tsv │ ├── miniali.tsv │ ├── remove_divergent.tsv │ ├── remove_gap_only.tsv │ ├── remove_insertions.tsv │ └── remove_short.tsv ├── example_files ├── example1.fasta ├── example2.fasta ├── example3.fasta └── example4.fasta ├── extra_scripts ├── checkMemoryAndTime.py ├── make_ini_template.py ├── param_groups.txt └── run_homfam.sh ├── index.rst ├── man ├── CIAlign_poster.pdf ├── Guidelines.pdf ├── Makefile ├── _static │ └── custom.css ├── adding_a_new_parameter.md ├── conf.py ├── contents.rst ├── images │ ├── CBS_small.png │ ├── bright_small.png │ ├── changefreq.png │ ├── cov_small.png │ ├── example.png │ ├── ic_small.png │ ├── identity.png │ ├── mini_small.png │ ├── resfreq.png │ ├── resfreq_nt.png │ ├── se_small.png │ ├── sequence_logo_bar_small.png │ ├── sequence_logo_small.png │ └── similarity.png ├── index.rst ├── legacy │ └── user_guide_template.md ├── make.bat ├── pages │ ├── installation.md │ ├── introduction.md │ └── usage.md ├── requirements.txt ├── update_manual.py └── user_guide_template_hold.md ├── pyproject.toml ├── requirements.txt ├── setup.py ├── templates └── ini_template.ini └── tests ├── __init__.py ├── consensusSeqTest.py ├── cropSeqTest.py ├── helperFunctions.py ├── miniAlignmentsTest.py ├── palettesTest.py ├── parsingFunctionsTest.py ├── pwmTest.py ├── similarityMatrixTest.py ├── test_files ├── alpha_aa.npy ├── alpha_aa_calc.npy ├── alpha_dna.npy ├── alpha_dna_calc.npy ├── alpha_rna.npy ├── alpha_rna_calc.npy ├── complex_crop_ends_cleaned.fasta ├── complex_insertions_cleaned.fasta ├── complex_parsing.fasta ├── complex_remove_divergent_cleaned.fasta ├── consensus_example_aa.fasta ├── consensus_example_aa_gaps.fasta ├── consensus_example_long.fasta ├── consensus_example_nt.fasta ├── corrupt.fasta ├── crop_divergent_cleaned.fasta ├── crop_divergent_cleaned2.fasta ├── crop_ends_cleaned.fasta ├── empty.fasta ├── example1.fasta ├── example2.fasta ├── example2_crop_ends_clean.fasta ├── example3_section.fasta ├── example3_section_large.fasta ├── expected_changecount.png ├── expected_identity_aa.png ├── expected_identity_nt.png ├── expected_mini_ali.png ├── expected_mini_ali_aa.png ├── expected_mini_ali_markup.png ├── expected_resfreq_aa.png ├── expected_resfreq_nt.png ├── expected_similarity_aa.png ├── expected_similarity_aa_PAM10.png ├── expected_similarity_nt.png ├── expected_similarity_nt_NUC.4.2.png ├── freq_aa.npy ├── freq_dna.npy ├── freq_rna.npy ├── keep.txt ├── keep_m.txt ├── meme_aa.out ├── meme_dna.out ├── meme_rna.out ├── nonIUPAC.fasta ├── overlap_crop_ends_cleaned.fasta ├── pfm_aa.tsv ├── pfm_dna.tsv ├── pfm_dna_large.tsv ├── pfm_rna.tsv ├── ppm_aa.tsv ├── ppm_dna.tsv ├── ppm_rna.tsv ├── pwm_aa.tsv ├── pwm_dna.tsv ├── pwm_rna.tsv ├── remove_divergent_cleaned.fasta ├── remove_gaponly_cleaned.fasta ├── remove_insertions_cleaned.fasta ├── 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