GitHub - millanek/evo: A loose set of tools for (mainly evolutionary) genomics

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A loose set of tools for (mainly evolutionary) genomics

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Name		Name	Last commit message	Last commit date
Latest commit History 538 Commits
Build		Build
Makefile		Makefile
Makefile_backup		Makefile_backup
YlikeCounts.txt		YlikeCounts.txt
evo_ABS.cpp		evo_ABS.cpp
evo_ABS.h		evo_ABS.h
evo_AlleleFeq.cpp		evo_AlleleFeq.cpp
evo_AlleleFeq.h		evo_AlleleFeq.h
evo_DNA_to_Protein.cpp		evo_DNA_to_Protein.cpp
evo_DNA_to_Protein.h		evo_DNA_to_Protein.h
evo_DegenerateSites.cpp		evo_DegenerateSites.cpp
evo_DegenerateSites.h		evo_DegenerateSites.h
evo_Dmin.cpp		evo_Dmin.cpp
evo_Dmin.h		evo_Dmin.h
evo_Dmin_combine.cpp		evo_Dmin_combine.cpp
evo_Dmin_combine.h		evo_Dmin_combine.h
evo_FstAgainstAll.cpp		evo_FstAgainstAll.cpp
evo_FstAgainstAll.h		evo_FstAgainstAll.h
evo_PBS.cpp		evo_PBS.cpp
evo_PBS.h		evo_PBS.h
evo_abba_baba.cpp		evo_abba_baba.cpp
evo_abba_baba.h		evo_abba_baba.h
evo_agpToNewFasta.cpp		evo_agpToNewFasta.cpp
evo_agpToNewFasta.h		evo_agpToNewFasta.h
evo_codingSeqs_fromGenomes.cpp		evo_codingSeqs_fromGenomes.cpp
evo_codingSeqs_fromGenomes.h		evo_codingSeqs_fromGenomes.h
evo_codingStats_from_alignment.cpp		evo_codingStats_from_alignment.cpp
evo_codingStats_from_alignment.h		evo_codingStats_from_alignment.h
evo_combineVCFs.cpp		evo_combineVCFs.cpp
evo_combineVCFs.h		evo_combineVCFs.h
evo_distanceToOutgroups.cpp		evo_distanceToOutgroups.cpp
evo_distanceToOutgroups.h		evo_distanceToOutgroups.h
evo_diversityFromHaps.cpp		evo_diversityFromHaps.cpp
evo_diversityFromHaps.h		evo_diversityFromHaps.h
evo_diversity_subsampling.cpp		evo_diversity_subsampling.cpp
evo_diversity_subsampling.h		evo_diversity_subsampling.h
evo_findDiscordantPairs.cpp		evo_findDiscordantPairs.cpp
evo_findDiscordantPairs.h		evo_findDiscordantPairs.h
evo_findDiscordantPairsFromSAM.cpp		evo_findDiscordantPairsFromSAM.cpp
evo_findDiscordantPairsFromSAM.h		evo_findDiscordantPairsFromSAM.h
evo_fullAnnotationExtract.cpp		evo_fullAnnotationExtract.cpp
evo_fullAnnotationExtract.h		evo_fullAnnotationExtract.h
evo_getInformativePairs.cpp		evo_getInformativePairs.cpp
evo_getInformativePairs.h		evo_getInformativePairs.h
evo_getInformativeReadsFromSam.cpp		evo_getInformativeReadsFromSam.cpp
evo_getInformativeReadsFromSam.h		evo_getInformativeReadsFromSam.h
evo_permute_codons.cpp		evo_permute_codons.cpp
evo_permute_codons.h		evo_permute_codons.h
evo_protein_SegregatingSites.cpp		evo_protein_SegregatingSites.cpp
evo_protein_SegregatingSites.h		evo_protein_SegregatingSites.h
evo_recombUtils.cpp		evo_recombUtils.cpp
evo_recombUtils.h		evo_recombUtils.h
evo_shared_variation.cpp		evo_shared_variation.cpp
evo_shared_variation.h		evo_shared_variation.h
excludeNoGenotypeCall.cpp		excludeNoGenotypeCall.cpp
extract_target_sequence_from_UTR.cpp		extract_target_sequence_from_UTR.cpp
extract_target_sequence_from_UTR.h		extract_target_sequence_from_UTR.h
extract_target_sequence_from_UTR_backup.cpp		extract_target_sequence_from_UTR_backup.cpp
extract_target_sequence_from_UTR_backup2.cpp		extract_target_sequence_from_UTR_backup2.cpp
filter_annotation.cpp		filter_annotation.cpp
filter_annotation.h		filter_annotation.h
gzstream.cpp		gzstream.cpp
gzstream.h		gzstream.h
nonZeroYlikeCounts.txt		nonZeroYlikeCounts.txt
process_vcf.1		process_vcf.1
process_vcf.cpp		process_vcf.cpp
process_vcf_IUPAC.cpp		process_vcf_IUPAC.cpp
process_vcf_IUPAC.h		process_vcf_IUPAC.h
process_vcf_annotation_tools.cpp		process_vcf_annotation_tools.cpp
process_vcf_annotation_tools.h		process_vcf_annotation_tools.h
process_vcf_cbs.cpp		process_vcf_cbs.cpp
process_vcf_cbs.h		process_vcf_cbs.h
process_vcf_coding_sequences.cpp		process_vcf_coding_sequences.cpp
process_vcf_coding_sequences.h		process_vcf_coding_sequences.h
process_vcf_fill_aa.cpp		process_vcf_fill_aa.cpp
process_vcf_fill_aa.h		process_vcf_fill_aa.h
process_vcf_filter.cpp		process_vcf_filter.cpp
process_vcf_filter.h		process_vcf_filter.h
process_vcf_fst.cpp		process_vcf_fst.cpp
process_vcf_fst.h		process_vcf_fst.h
process_vcf_get_aa_seq.cpp		process_vcf_get_aa_seq.cpp
process_vcf_get_aa_seq.h		process_vcf_get_aa_seq.h
process_vcf_get_sequences.cpp		process_vcf_get_sequences.cpp
process_vcf_get_sequences.h		process_vcf_get_sequences.h
process_vcf_join_multiFasta.cpp		process_vcf_join_multiFasta.cpp
process_vcf_join_multiFasta.h		process_vcf_join_multiFasta.h
process_vcf_linkGeneNames.cpp		process_vcf_linkGeneNames.cpp
process_vcf_linkGeneNames.h		process_vcf_linkGeneNames.h
process_vcf_massoko.cpp		process_vcf_massoko.cpp
process_vcf_massoko.h		process_vcf_massoko.h
process_vcf_merge.cpp		process_vcf_merge.cpp
process_vcf_merge.h		process_vcf_merge.h
process_vcf_mt_sequences.cpp		process_vcf_mt_sequences.cpp
process_vcf_mt_sequences.h		process_vcf_mt_sequences.h
process_vcf_polymorphic_in_sets.cpp		process_vcf_polymorphic_in_sets.cpp
process_vcf_polymorphic_in_sets.h		process_vcf_polymorphic_in_sets.h
process_vcf_print_routines.cpp		process_vcf_print_routines.cpp
process_vcf_print_routines.h		process_vcf_print_routines.h
process_vcf_reorder.cpp		process_vcf_reorder.cpp
process_vcf_reorder.h		process_vcf_reorder.h