This repository provides the ncessary scripts to construct a species tree based on large sequence data sets of a number of different species. The tree will show the phylogenetic relationships of these species.
This script extracts all BUSCOs that are present with exactly one copy from a given BUSCO run result folder.
python3 get_single_copy_BUSCOs.py --busco <FILE> --pepin <FILE> --pepout <FILE>
Arguments:
--busco STR BUSCO result TSV file
--pepin STR Peptide input file
--pepout STR Peptide output file
--busco specifies the central BUSCO result file (TSV). This file provides the IDs of single copy orthologs in the given species. IDs in this file need to match the provided peptide sequence input file.
--pepin specifies the polypeptide sequence input file (FASTA). The sequences of single copy ortholog IDs will be retrieved from this file.
--pepout specifies the polypeptide sequence output file (FASTA). The sequences of single copy ortholog IDs will be written into this file.
Construct a phylogenetic tree based on all sequences across the species of interest.
python3 phyl_constr.py --baits <FILE> --in <FILE> --out <DIRECTORY>
Arguments:
--baits STR Bait sequence file
--in STR Config file
--out STR Output folder
optional:
--mode STR Analysis mode (cds|prot)[cds]
--blastp STR Path to blastp[blastp]
--makeblastdb STR Path to makeblastdb[makeblastdb]
--fasttree STR Path to FastTree2[FastTree]
--mafft STR Path to MAFFT[mafft]
--minsim FLOAT Minimal BLASTp hit similarity[80.0]
--minlen INT Minimal BLASTp hit length[50]
--repratio FLOAT Minimal ratio of represented species per gene tree[1.0]
--occupancy FLOAT Minimal alignment occupancy[0.1]
--baits specifies a FASTA input file.
--in specifies a config input file.
--out specifies an output folder. This folder will be created if it does not exist already.
--mode specifies the analysis mode. This needs to indicate whether the input comprizes coding sequences (cds) or polypeptide sequences (prot). Default: cds.
--blastp specifies the full path to the blastp binary. This variable can be used if blastp is not accessbile through your PATH variable. Default: blastp.
--makeblastdb specifies the full path to the makeblastdb binary. This variable can be used if blastp is not accessbile through your PATH variable. Default: makeblastdb.
--fasttree specifies the full path to the FastTree2 binary. This variable can be used if FastTree2 is not accessbile through your PATH variable. Default: fasttree.
--mafft specifies the full path to the MAFFT binary. This variable can be used if MAFFT is not accessbile through your PATH variable. Default: mafft.
--minsim specifies the minimal similarity of a BLAST hit to be considered in the following analysis. Default: 80.0.
--minlen specifies the minimal length of a BLAST hit to be considered in the following analysis. Default: 50.
--repratio specifies the number of species that need to contribute an ortholog to a set of sequences. Only sets of orthologous sequences with a sufficient ratio of representated species are considered for the phylogenetic tree construction. Default: 1.0 (all).
--occupancy specifies the minimal alignment occupancy. This determines which columns will be removed during the alignment trimming step. Default: 0.1.
This repository.