FMAlign
a fast multiple nucleotide sequence alignment method based on FM-index

How to use FMAlign
Download:

git clone https://github.com/iliuh/FMAlign.git
or download ZIP package

Build:

cd FMAlign
make

Usage:

./FMAlign [options]

• General Options:
  --help Show the help file.

• Options of alignment:
  --in [filename] Input the sequences file in FASTA format
  --out [file] Output of the aligned sequences in FASTA format. The default "output" is filename.fmalign.
  --thread [int] Set the number of CPU threads (default: 1).
  --package Aligning the sub-sequences by MSA tool, mafft or halign. The default "package" is mafft.

notice： if package mafft can not work, please type

cd packages/MAFFT
make

Related tools:

• SP is a jar file that was used in our experiment, it is used to compute the average value of sum-of-pair score for the alignment result. http://lab.malab.cn/soft/halign/
• The FMtree library that was used in our work, FMtree is an improved FM-INDEX based on tree. https://github.com/chhylp123/FMtree