wpsboot's Introduction

wpSBOOT

weighted partial super bootstrap

src/concatenate.pl

Union concatenate alignments according to inputting order into a Super-MSA with PHYLIP format.

requirement

Please install the following modules from BioPerl. Detailed information in BioPerl.

Bio::AlignIO
Bio::Align::Utilities
Bio::LocatableSeq

>perl -MCPAN -e shell
cpan> install Bio::AlignIO

usage

concatenate.pl [options] --aln alignment1 alignment2 ... (at least two alignments) --out result
	--intersect: only concatenate sequences appearing in all alignments, otherwise missing sequence is replaced with gap (default)
	--random: concatenate order is random
	--size N: only concatenate first N alignments from inputting, exclusive with replicate mode
	--replicate NUM: replicate one alignment in NUM times, exclusive with size mode

an example commend

perl concatenate.pl --aln MAFFT.fasta Muscle.fasta ClustalW.fasta T-Coffee.fasta --out superMSA.phylip

corresponding running log

How to concatenate:
	size: 4 alignments
	alignments:
		MAFFT.fasta
		Muscle.fasta
		ClustalW.fasta
		T-Coffee.fasta
	output: superMSA.phylip

web server

https://wpsboot.page.link/main

reference

original paper: J.-M. Chang, E. W. Floden, J. Herrero, O. Gascuel, P. Di Tommaso, and C. Notredame, Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability. Bioinformatics, Feb. 2019
related work: H Ashkenazy, I Sela, E Levy Karin, G Landan, T Pupko, Multiple sequence alignment averaging improves phylogeny reconstruction. Systematic biology, 2019 68 (1), 117-130

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wpsboot's Issues

uncleat functionality

My idea was to use this script to make a concatenated MSA and bootstrap it with the subsamples lengths equal to the mean length of individual MSAs used (as it is actually written in Chang 2021 paper), however, it seems that the present script make a concatenated MSA only. Am I correct or I did not get how to bootstrap/subsample this concatenated MSA using the script?

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