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4 Commits
00_PATRON_fasta2phylip.py
00_PATRON_fasta2phylip.py
 
 
01_RemoveTooShort_bit_or_whole_sequence_v1.0.py
01_RemoveTooShort_bit_or_whole_sequence_v1.0.py
 
 
01_concatenate_v3.0.py
01_concatenate_v3.0.py
 
 
01_get_locus_ortholog_part1.py
01_get_locus_ortholog_part1.py
 
 
01_merge_paired_fastq_v4.0.py
01_merge_paired_fastq_v4.0.py
 
 
02_format_fasta_name_TRINITY.py
02_format_fasta_name_TRINITY.py
 
 
02_uninterleave_fasta_in_file_and_format_fastaName.py
02_uninterleave_fasta_in_file_and_format_fastaName.py
 
 
03_findORF_onMultipleAlignment_v2.py
03_findORF_onMultipleAlignment_v2.py
 
 
03_get_locus_ortholog_part2.py
03_get_locus_ortholog_part2.py
 
 
03_organize_RBH.py
03_organize_RBH.py
 
 
03_run_BLAST_with.K.filter.sh
03_run_BLAST_with.K.filter.sh
 
 
03_study_seq_composition_NUC_v3.1.py
03_study_seq_composition_NUC_v3.1.py
 
 
04_Choose_One_variants_per_locus_TRINITY_v1.0.py
04_Choose_One_variants_per_locus_TRINITY_v1.0.py
 
 
04_study_seq_composition_AA_v4.1.py
04_study_seq_composition_AA_v4.1.py
 
 
05_scriptExtractMatch_v20_BLASTX.py
05_scriptExtractMatch_v20_BLASTX.py
 
 
06_1_unInterleave_BigFastaFile_and_ShorteningFastaName.py
06_1_unInterleave_BigFastaFile_and_ShorteningFastaName.py
 
 
06_format_fasta_name_TRINITY.py
06_format_fasta_name_TRINITY.py
 
 
06_joinContigsAndSinglets.py
06_joinContigsAndSinglets.py
 
 
07_removeSiteWithNotEnoughSpeciesRepresented_v2.0.py
07_removeSiteWithNotEnoughSpeciesRepresented_v2.0.py
 
 
08_1_postProcessing_of_pairwise_v3.0.py
08_1_postProcessing_of_pairwise_v3.0.py
 
 
08_2_formatMatch_getBackNucleotides_v2.py
08_2_formatMatch_getBackNucleotides_v2.py
 
 
09_OrganizeFolders_AND_run_SIXTET.py
09_OrganizeFolders_AND_run_SIXTET.py
 
 
10_run_BLAST2_with.K.filter.sh
10_run_BLAST2_with.K.filter.sh
 
 
11_extract_PositivelySelected_Sites_v4.0_freeRatios.py
11_extract_PositivelySelected_Sites_v4.0_freeRatios.py
 
 
12_scriptExtractMatch_v20_BLASTX.py
12_scriptExtractMatch_v20_BLASTX.py
 
 
14_postProcessing_of_pairwise_v3.0.py
14_postProcessing_of_pairwise_v3.0.py
 
 
16_compareListPairs_forReciprocalBestHitsTest_v3.1.py
16_compareListPairs_forReciprocalBestHitsTest_v3.1.py
 
 
17_stats_withR.py
17_stats_withR.py
 
 
18_postProcessing_of_pairwise_v4.0.py
18_postProcessing_of_pairwise_v4.0.py
 
 
19_PutAllBranchResultsInOneTable.r
19_PutAllBranchResultsInOneTable.r
 
 
24_PROT2DNA_v2.2.py
24_PROT2DNA_v2.2.py
 
 
24_prepare_BlastAlignRuns.py
24_prepare_BlastAlignRuns.py
 
 
LICENSE
LICENSE
 
 
README.md
README.md
 
 
XXX_patronPipeline.sh
XXX_patronPipeline.sh
 
 
blastalign.py
blastalign.py
 
 
count_lines.py
count_lines.py
 
 
count_sequences.py
count_sequences.py
 
 
phylip2fasta.py
phylip2fasta.py
 
 
remove_redondancy_from_oases_output_v3.0.py
remove_redondancy_from_oases_output_v3.0.py
 
 

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A pipeline for the search of adaptive mutations and positively selected genes from RNASeq orthologs

www.sb-roscoff.fr/fr/abice-adaptation-et-biologie-des-invertebres-en-conditions-extremes

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