justincbagley/MAGNET: MAGNET version 1.2.0

<a href="http://imgur.com/KyBBOwk"><img src="http://i.imgur.com/KyBBOwk.png" title="source: Justin C. Bagley" width=60% height=60% align="center" /></a>

Shell script pipeline for inferring ML gene trees for many loci (e.g. RAD loci, UCEs)

This is MAGNET (MAny GeNE Trees) v1.2.0, a shell script pipeline within the PIrANHA software package (Bagley 2020) whose goal is to automate inferring a maximum-likelihood (ML) gene tree in RAxML v8+ (Stamatakis 2014) for each locus in a multilocus dataset. Prior to the present major version release, this repository was in development with the only releases available being pre-releases (up to v0.1.4), and the scripts had not been updated in a while. This new v1.2.0 release is a stable major release (versioned up through v1.0 within PIrANHA) that is greatly improved and ready for use in phylogenetics or phylogenomics workflows! Improvements include code edits, bug fixes, and the long option flags for all options of MAGNET (see the README or verbose help text (./MAGNET -H) for additional information).

MAGNET is currently only being actively maintained and developed within PIrANHA, where it is at v1.2.0. The present repository will be periodically updated to include a standalone version of the MAGNET software. This helps users interested only in MAGNET; however, it is strongly recommended that you install the full PIrANHA distribution (which comes with MAGNET) and request MAGNET updates or bug fixes through the PIrANHA repo (e.g. contact the author, or raise an issue here).

Consider:

• Expanding MAGNET to give users the option to infer ML gene trees with other programs. Here, a great addition would be allowing users to estimate gene trees for many loci using IQ-TREE v2+.
• Adding bash tab completion of option suggestions.
• Adding conditionals to specifically accommodate case of a single input PHYLIP file (currently this is covered by -f 2 routine, because looping through a single file accomplishes the same thing; however, if a new option or set of conditions were implemented for a single input PHYLP file then it could combined with -p flag suggested in next item).
• -p|--part flag to allow partitioned analysis, in the case of single input PHYLIP file.

• Bagley, J.C. 2020. PIrANHA v0.4-alpha4. GitHub repository, Available at: http://github.com/justincbagley/piranha/.
• Stamatakis, A. 2014. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30.9, 1312-1313.