'phyloGenerator-light' or pG-lt is a python package for the automated generation of phylogenies from multiple lists of taxon names.

The package implements a pipeline that uses 'mass phylogeny estimation' to generate distributions of phylogenies from multiple sequences and alignments with minimum human-input.

The pipeline consists of four stages: names resolution, sequence download, sequence alignment and phylogeny estimation.

pG-lt is a member of the phyloGenerator family.

Available on pip: pip install pglt.

Set dependencies: pglt_set_dependencies.py

Run: run_pglt.py -e [EMAIL ADDRESS]

See wiki for further information on how to use and install.

• One-line implementation: run_pglt.py -e [EMAIL ADDRESS]
• Automatic or user specified parameters
• Fuzzy taxonomic name matching
• Automatic outgroup selection
• Heuristic gene selection
• Automatic sequence download with taxonomic context
• Heuristic alignment and phylogeny checking
• Rate partitioning between genes and codon positions
• HPC compatible
• Runs on Windows, OSX and Linux

• Alignment tools: MAFFT and stand-alone BLAST
• Phylogeny tools: RAxML

pG-lt is still in its developmental stage.

GPL v.2

Dom Bennett, Will Pearse, Lawrence Hudson, Gerard Gorman and Andy Purvis