Phylogenetic Focusing Revelas the Evolution of Eumetazoan Opsins

Deep analyses of eumetazoan opsin phylogeny

See COMMANDLINE.md for list of commands and arguments used for analyses

Scripts used for Phylogenetic Focusing

0_makeblast.sh

Shell script for formatting fastas into blastable databases

1_blast.sh

Shell script for BLASTp search against blast dbs with a fasta containing query seqs. Retrieves the sequence data back

2_concat_ali.sh

Shell script, runs CD-HIT to remove redundancy, adds bait and anchor seqs in, and aligns using MAFFT

3_convert.sh

Shell script using the perl seqConverter.pl script to convert alignment files to phylip

4_RAxML.sh

Shell script making ML trees using PROTGAMMAGTR model in RAxML. Must be executed in directory containing phylip files

5_tree_editor.R

R script for first round of phylogenetic focusing. Filtering out distantly related sequences in a taxon specific manner

6_pull_seqs.sh

(loop under construction). Shell script for retrieving sequence data for all the genes that were included in the trees export from tree_editor.R script

7_total_ali_and_tree.sh

Shell script to concatenate all fastas together into the "total" dataset and aligns using MAFFT

selectSeqs.pl

Perl script: you provide file with the names of sequences wanted, the original fasta containing all the sequence data, and it outputs a fasta file containing the sequence data only from the names you provided

seqConverter.pl

Perl script for converting alignments into phylip files

name_change.py

Python script for changing names back to original format after the alignment program PASTA strips capital letters and underscores

branch_trimmer.py

Python script for pruning branches that exceed a user defined branch length in a phylogeny

seqRemover.py

Python script: given a fasta file and the text file containing the headers of unwanted seqs, this script outputs a new file lacking the unwamted seqs specified in the text file