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GLaMST

This algorithm is developed to reconstruct lineage tree from subset of tree nodes.

Download

GLaMST can be downloaded from https://github.com/xysheep/GLaMST/releases

Usage of Source code

A simple demonstration of how to use the source code is avaliable at https://xysheep.github.io/GLaMST . If Matlab is not avaliable to you, you can use the pre-compiled version. The compiled version is slightly slower than the source code.

As a note, the "main.m" is used to generate the pre-compiled file. "index.m" is used to generate the demonstration page.

Usage of pre-compiled executible

To use this executable, the MATLAB Runtime 9.2 is required. It can be downloaded from here. This executible is only for Windows users.

GLaMST.exe fastafilename [...options]

Arguments

Required Arguments

  • fastafilename: name of one fasta file. The first sequence in the fasta file should be root (G. L.). Sequences in this fasta file should be original assembled sequences, not multiple alignment results.

Optional Arguments

  • rewire: 1 means do rewire while 0 means not do rewire [default 1]