BuscoOrthoPhylo

Wrapper for Phylogenetic construction of BUSCO orthologs

Summary

This is a wrapper script that takes multiple BUSCO output folders or the output folder from Orthofinder to concatenate, align, and contruct phylogentic tree(s) of single copy BUSCOs/orthologs. Please be aware of directory strucuture required for BUSCO innput (see below)

Dependencies

1. MAFFT or MUSCLE
2. FastTree or RAxMLHPC-PTHREADS

Usage

optional arguments:
  -h, --help                                show this help message and exit
  -d , --directory                          Parent directory containing directory for each species
  -i , --input                              Program used for input directory data [busco|orthofinder]
  -o , --out                                Name for output directory
  -k , --key                                Keyword to help find correct BUSCO output folder [ex. -k sordario when busco output folder is run_sordario
  -t , --type                               Choice of sequence output [prot|nuc|both] (only prot available when using orthofinder)[default: prot]
  -sub , --subsample                        Percent of genes to subsample for a preliminary analysis [ex. 0.10]
  -l , --list                               File contains list of single copy BUSCOs or Orthogroups for Phylogeny on (one per line)
  --stop                                    Stop after concatenation [ac] stop after alignment [aa]
  --resume                                  Resume after concatenation [ac] resume after alignment [aa]
  -c , --cpus                               Cores to use [default: 2]
  -a , --aligner                            Choice of sequence aligner [mafft|muscle] [default: mafft]
  -ma_a  [ ...], --mafft_args  [ ...]       Additional flags, separated by commas, within quotes, no spaces after commas, to be used in MAFFT alignment [ex. 'localpair,maxiterate 0-1000']
  -mu_i , --muscle_iter                     Maximum number of iterations for MUSCLE [default: 16]
  -mu_d, --muscle_diags                     Turn on find diagonals for MUSCLE (faster for similar sequences) [default: OFF]
  -ph , --phylogeny                         Choice of sequence output [fasttree|raxml] [default: fasttree]
  -b , --boot                               Number of bootstraps. Seriously consider reducing if using raxml. [default: 1000]
  -ft_a  [ ...], --fasttree_args  [ ...]    Additional flags, separated by commas, within quotes, no spaces after commas,to be used in fasttree run [ex. 'slow,bionj,spr 4']
  -rx_a  [ ...], --raxml_args  [ ...]       Additional flags, separated by commas, within quotes, no spaces after commas,to be used in raxml run [ex. 'k,f a,t file.nwk']
  -rx_og  [ ...], --raxml_outgroup  [ ...]  Names of outgroup species to use in raxml run [ex. 'rat,mouse,fly,human']. Names must correlate to headers in alignment file
  -rx_p_sub , --raxml_prot_sub              Protein substitution model to use [see raxmlHPC -h for all -m flag options] [default: PROTCATAUTO]
  -rx_n_sub , --raxml_nuc_sub               Nucleotide substitution model to use [see raxmlHPC -h for all -m flag options] [default: GTRCAT]
  -rx_al , --raxml_algorithm                Algorithm to use [see raxmlHPC -h for all -f flag options] [default: a]
  -rx_t, --raxml_threads                    Turn off PTHREADS [default: ON]

For BUSCO use please set up your Parent_directory (-d/--directory input) like so:

Parent_directory
    |
    |
    |
    +--Genus_species  <- This name will be used in FASTA headers and Phylogenetic trees
    |       |
    |       |
    |       +--run_xxx  <- This is your BUSCO output folder
    |
    |
    +--Genus_species
            |
            |
            +--run_xxx

For Orthofinder use:

Parent_directory = Results_XXX output folder from Orthofinder

(Note: Orthofinder will only use 'prot' as Orthofinder does not output any nucleotide sequences)

(Note: Currently only compatible with Orthofinder Version 2.2 or lower. Will add 2.3 and above soon)

Default commands

Running the script with all default settings will run these commands depending on which aligner and ML construction program you use.

MAFFT

mafft --threads 2 genes.fasta > alignment.fasta

MUSCLE

muscle -maxiters 16 -log logfile.log -in genes.fasta -out alignment.fasta

FastTree

1. Proteins

FastTree -seed 12345 -gamma -boot 1000 -log logfile.log alignment.fasta > tree.nwk

2. Nucleotides

FastTree -nt -seed 12345 -gamma -boot 1000 -log logfile.log alignment.fasta > tree.nwk

RAxML (It is highly recommended to reduce the bootstraps for RAxML with -b/--boot flag or you could be waiting a very very long time)

1. Proteins

raxmlHPC-PTHREADS -m PROTCATAUTO -s alignment.fasta -x 12345 -p 12345 -# 1000 -k -T 2 -f a -n prot_out

2. Nucleotides

raxmlHPC-PTHREADS -m GTRCAT -s alignment.fasta -x 12345 -p 12345 -# 1000 -k -T 2 -f a -n prot_out

Output files

Output Folder

1. species

   • Individual species folders containing FASTA file of genes and concatenation of genes

2. alignment

   • Final FASTA concatenation of all species and alignment FASTA file(s)

3. phylogeny

   • Newicks tree file(s) and other associated files