Collection of little scripts for wrangling files before a phylogenetic analysis.
| Script | Useful for you? | Description |
|---|---|---|
| aln_to_subtree | yes | remove taxa from a tree to match those in an alignment. |
| domain_chop | no | divide 4 domain protein into constituent domains. Used in Liebeskind et al. 2013 |
| ensembl_tsv_ids | no | for parsing tab delimited files downloaded from Ensembl after an ortholog search |
| entrez_xml_mods | no | functions for dealing with entrez xml. Most are broken |
| fas_to_nex | yes | convert fasta file to nexus |
| fas_to_phy | yes | convert fasta file to phylip (good for PAML) |
| hmmalign_parser | no | parse a stockholm alignment output by hmmer |
| keepers_subAlnTree | yes | get a subalignment and tree with an text file of taxa you wish to retain |
| longest_cds | yes | for getting longest transcripts from files of Ensembl genes with multiple transcripts |
| open_reading_fram | yes | get longest open reading frames for each sequence in a fasta file (good for NGS data but only looks at forward frame, so it works for RNAseq) |
| phylip_map | maybe | replace long description lines with short names, and keep track of changes |
| remove_redundant | yes | remove redundant sequences from a sequence file |
| stockholm_pps | no | explore posterior probabilities on stockholm alignment such as those put out by hmmer |
| TPC_chop | no | divide 2 domain protein into constituent domains. Used in Liebeskind et al. 2013 |