goalign

GoAlign

GoAlign is a set of command line tools to manipulate phylogenetic trees. It is implemented in Go language.

Installation

Binaries

You can download already compiled binaries for the latest release in the release section. Binaries are available for MacOS, Linux, and Windows (32 and 64 bits).

Once downloaded, you can just run the executable without any other downloads.

From sources

In order to compile GoAlign, you must first download and install Go on your system.

Then you just have to type :

go get github.com/fredericlemoine/goalign/

This will download GoAlign sources from github, and all its dependencies.

You can then build it with:

cd $GOPATH/src/github.com/fredericlemoine/goalign/
make

The goalign executable should be located in the $GOPATH/bin folder.

Usage

List of commands

• addid: Adds a string to each sequence identifier of the input alignment
• build: Command to build output files : bootstrap for example
  • seqboot : Generate bootstrap alignments
• clean: Removes gap sites
• compute: Different computations (distances, etc.)
  • distances: compute evolutionary distances for nucleotide alignment
• divide: Divide an input alignment in several output files (one per alignment)
• random: Generate random sequences
• reformat: Reformats input alignment into phylip of fasta format
  • fasta
  • nexus
  • phylip
  • tnt
• rename: Rename sequences of the input alignment, given a map file
• sample: Randomly samples a subset of sequences from the input alignment
• shuffle: A set of commands to shuffle an alignment
  • recomb: Recombine some sequences (copy/paste)
  • seqs: Shuffle sequence order in the alignment
  • sites: Shuffle "vertically" some sites of the alignments
  • swap: Swap portions of some sequences (cut/paste)
• stats: Prints different characteristics of the alignment
  • alleles
  • char
  • length
  • nalign
  • nseq
  • taxa
• subset: Take a subset of sequences from the input alignment
• trim: This command trims names of sequences or sequences themselves
  • name
  • seq
• unalign: Unaligns input alignment
• version: Prints the current version of goalign

Examples

• Generate a random alignemnt and print statistics

goalign random | goalign stats

• Trim names of a random alignment and finally rename it back

goalign random > align.fa
goalign trim name -n 3 -m map -i align.fa > align_rename.fa
goalign rename -i align_rename.fa -m map -r 

• Reformat a fasta alignment to phylip

goalign random | goalign reformat phylip

• Reformat a phylip alignment to fasta

goalign random -p | goalign reformat fasta -p

• Add a prefix to all sequence names of the alignment

goalign random  | goalign addid -n "Dataset1_" 

• Add a suffix to all sequence names of the alignment

goalign random  | goalign addid -r -n "_Dataset1" 

• Take a random sample (10 sequences) from an input alignment

goalign random -n 10000 | goalign sample -n 10

• Build 100 bootstrap alignments from an input alignment, in a single tar.gz file (5 threads)

goalign random -n 500 | goalign build seqboot -S -n 100 --gz --tar -t 5 -o boot

• Build 100 bootstrap alignments from an input alignment, in 100 .gz files (5 threads)

goalign random -n 500 | goalign build seqboot -S -n 100 --gz -t 5 -o boot