MAGNET version 1.2.0

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).

NOTICE

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).

TO-DO

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.

REFERENCES

• 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.

MAGNET version 0.1.4

MAGNET v0.1.4 🌳🌳🌳

This is MAGNET v0.1.4.

• MAGNET stands for "MAny GeNE Trees."
• This release includes updated Usage sections in the MAGNET.sh script and README; new flags for regular (-h, -help) and verbose help/usage info (-H, -Help) pointing to rewritten help texts; as well as other minor updates and improvements to the README and scripts (e.g. removed instances of echoed lists being used to identify files with specific extensions, now use find instead; attempt to use grep -E instead of now-deprecated egrep). This software remains under testing and development.

MAGNET version 0.1.3

MAGNET v0.1.3 🌳🌳🌳

This is MAGNET v0.1.3.

• MAGNET stands for "MAny GeNE Trees."
• This release includes the first draft of a new utility phyNcharSumm.sh for summarizing information about the number of characters across (SNP) loci processed in MAGNET, which is now located in the shell folder of the distribution. This software is under active development, so expect other minor fixes and improvements likely in coming days/weeks.

MAGNET version 0.1.2

MAGNET v0.1.2 🌳🌳🌳

This is MAGNET v0.1.2.

• MAGNET stands for "MAny GeNE Trees."
• This release includes a minor fix that improves the display of messages to screen by adding the date and time to instances where messages are echoed. This software is under active development, so expect other minor fixes and improvements likely in coming days/weeks.

MAGNET version 0.1.1

MAGNET v0.1.1 🌳🌳🌳

This is MAGNET v0.1.1.

• MAGNET stands for "MAny GeNE Trees."
• This release includes a minor fix to the code correcting line spacing in the .gphocs file created when MAGNET automatically detects an input .nex file and converts it to .gphocs. Other minor fixes and improvements likely in coming days/weeks.

MAGNET major version zero

MAGNET v0.1.0 🌳🌳🌳

This is MAGNET v0.1.0, major version zero for initial development. MAGNET stands for "MAny GeNE Trees." MAGNET is first being released to the public as v0 (and not a beta version) because it runs out of the box, with no bugs. However, this is a 0.1 release because this software may be in development, and new minor additions and fixes may be added soon, before a major version 1 release.