Skip to content

alexvasilikop/Rotifer_phylogeny

BranchesTags

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

7 Commits
LICENSE
LICENSE
 
 
README.md
README.md
 
 
check_monophyly_of_lineage_specific_gene_multiplications.py
check_monophyly_of_lineage_specific_gene_multiplications.py
 
 
delete_sequence_from_fasta.py
delete_sequence_from_fasta.py
 
 
delete_sequence_with_pattern_from_fasta.py
delete_sequence_with_pattern_from_fasta.py
 
 
extract_othogroups_multiple_copy_orthofinder_missing_taxa.py
extract_othogroups_multiple_copy_orthofinder_missing_taxa.py
 
 
extract_othogroups_single_copy_orthofinder_missing_taxa.py
extract_othogroups_single_copy_orthofinder_missing_taxa.py
 
 
extract_single_copy_othogroups_orthofinder.py
extract_single_copy_othogroups_orthofinder.py
 
 
filter_isoforms_NCBI.py
filter_isoforms_NCBI.py
 
 
filter_isoforms_NCBI_mod.py
filter_isoforms_NCBI_mod.py
 
 
keep_OGs_that_contain_all_clades_from_list.py
keep_OGs_that_contain_all_clades_from_list.py
 
 
keep_OGs_that_contain_all_clades_from_list_multi_copy_orthogroups.py
keep_OGs_that_contain_all_clades_from_list_multi_copy_orthogroups.py
 
 
keep_OGs_that_contain_multiple_copies_only_for_one_group.py
keep_OGs_that_contain_multiple_copies_only_for_one_group.py
 
 
keep_OGs_that_contain_multiple_copies_only_for_one_species.py
keep_OGs_that_contain_multiple_copies_only_for_one_species.py
 
 
keep_longest_trinity_transcript.py
keep_longest_trinity_transcript.py
 
 
remove_cds_seqs_not_present_in_pep_file.py
remove_cds_seqs_not_present_in_pep_file.py
 
 
remove_peptide_seqs_with_stop_codons.py
remove_peptide_seqs_with_stop_codons.py
 
 
remove_sites_private_amino_acids_for_two_specified_species_alignment.py
remove_sites_private_amino_acids_for_two_specified_species_alignment.py
 
 
remove_sites_with_private_amino_acids_one_species_alignment.py
remove_sites_with_private_amino_acids_one_species_alignment.py
 
 
replace_sequence_ID_with_gene_ID.py
replace_sequence_ID_with_gene_ID.py
 
 
retrieve_sequences_from_fasta.py
retrieve_sequences_from_fasta.py
 
 
select_best_fasta_subgroup_and_combine_with_other_sequences_in_orthogroup.py
select_best_fasta_subgroup_and_combine_with_other_sequences_in_orthogroup.py
 
 
select_trees_for_which_multiple_copies_of_bdelloids_are_monophyletic.py
select_trees_for_which_multiple_copies_of_bdelloids_are_monophyletic.py
 
 
select_trees_for_which_multiple_copies_of_bdelloids_are_monophyletic_and_make_pruned_trees.py
select_trees_for_which_multiple_copies_of_bdelloids_are_monophyletic_and_make_pruned_trees.py
 
 

Repository files navigation

Rotifer_phylogeny

custom scripts used to infer the syndermatan/rotiferan phylogeny in the following article:

Vasilikopoulos A. et al. 2024. Whole-genome analyses converge to support the Hemirotifera hypothesis within Syndermata (Gnathifera). Hydrobiologia. https://doi.org/10.1007/s10750-023-05451-9

About

rotifer phylogeny scripts

Resources

Readme

License

MIT license
Activity

Stars

0 stars

Watchers

1 watching

Forks

0 forks
Report repository

Releases

No releases published

Packages

No packages published

Languages