goalign

README

Goalign

Goalign is a set of command line tools to manipulate multiple alignments. It is implemented in Go language.

Goalign aims to handle multiple alignments in Phylip, Fasta, Nexus, and Clustal formats, through several basic commands. Each command may print result (an alignment for example) in the standard output, and thus can be piped to the standard input of the next goalign command.

Input files may be local or remote files:

• If file name is of the form http(s)://<URL>, the file is download from the given URL.
• Otherwise, the file is considered local.

Gzipped input files (.gz extension) are supported, as well as XZ files (.xz extension) and BZipped files (.bz[2] extension).

Note:

TO manipulate phylogenetic trees, See also Gotree.

Reference

If you use Gotree or Goalign, please cite:

Frédéric Lemoine, Olivier Gascuel

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows,

NAR Genomics and Bioinformatics, Volume 3, Issue 3, September 2021, lqab075, doi

Installation

Easy way: Binaries

You can download ready to run 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.

Docker

Goalign Docker image is accessible from docker hub. You may use it as following:

# Display goalign help
docker run -v $PWD:$PWD -w $PWD -i -t evolbioinfo/goalign:v0.2.6 -h

Singularity

Goalign docker image is usable from singularity . You may use it as following:

# Pull image from docker hub
singularity pull docker://evolbioinfo/goalign:v0.2.6
# Display goalign help
./goalign-v0.2.6.simg -h

Conda

Goalign is also available on bioconda. Just type:

conda install -c bioconda goalign

From sources

In order to build Goalign, you must first download and install Go on your system ($1.16.4$).

Then you just have to type :

go get github.com/evolbioinfo/goalign/

This will download Goalign sources from github.

You can then build it with:

cd $GOPATH/src/github.com/evolbioinfo/goalign/
make && make install

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

Auto completion

goalign uses cobra, and therefore proposes a command to generate auto completion scripts:

gotree completion -h

Usage

You may go to the doc for a more detailed documentation of the commands.

List of commands

• addid: Adds a string to each sequence identifier of the input alignment
• append: Concatenates several alignments by adding new alignments as new sequences of the first alignment
• build: Command to build output files : bootstrap for example
  • seqboot : Generate bootstrap alignments
• clean: Removes gap sites/sequences
  • sites : Removes sites with gaps
  • seqs : Removes sequences with gaps
• codonalign: Aligns a given nt fasta file using a corresponding aa alignment (by codons)
• compress: Removes identical patterns/sites from alignment
• compute: Different computations (distances, etc.)
  • distances: compute evolutionary distances for nucleotide alignment
  • entropy: compute entropy of alignment sites
  • pssm: compute position-specific scoring matrix
• concat: Concatenates several alignments by concatenating each sequences having the same name
• consensus: Compute a basic majority consensus of an input alignment
• dedup: Remove sequences that have the same sequence
• diff : Compare all sequences to the first one of the alignment, and count the differences
• divide: Divide an input alignment in several output files (one per alignment)
• draw: Draw alignments
  • biojs: Display an input alignment in an html file using BioJS
  • png: Display an input alignment in a png file, one sequence per line and one pixel per character
• extract: Extract several sub-alignments, potentially composed of several blocks, from an input alignment, using an coordinate file
• identical: Tell whether two alignments are identical
• mask: Replace positions by N (of nucleotides) or X (if amino-acids)
• mutate: Add substitutions (~sequencing errors), or gaps, uniformly in an input alignment
  • gaps: Add gaps uniformly in an input alignment
  • snvs: Add substitutions uniformly in an input alignment
• orf: Find the longest orf in all given sequences in forward strand
• phase: Try to find reference orf(s) (aa) in input sequences, and align it on the same phase
• phasent: Try to find reference sequence (nt) in input sequences, and align it on the same phase
• random: Generate random sequences
• reformat: Reformats input alignment into several formats
  • fasta
  • nexus
  • paml
  • clustal
  • phylip
  • tnt
• rename: Rename sequences of the input alignment, (using a map file, with a regexp, or just clean names)
• replace: Replace characters in sequences of input alignment using a regex
• sample: Samples sequences or subalignments
  • seqs: Randomly samples a subset of sequences from the input alignment
  • sites: Extracts a sub-alignment starting a a random position, and with a given length
  • rarefy: Down-samples input alignment, taking into accounts weights/counts of all sequences
• shuffle: A set of commands to shuffle an alignment
  • recomb: Recombine some sequences (copy/paste)
  • rogue: simulate sort of rogue taxa by shuffling some sequences
  • seqs: Shuffle sequence order in the alignment
  • sites: Shuffle "vertically" some sites of the alignments
  • swap: Swap portions of some sequences (cut/paste)
• split: Split an input alignment according to partitions defined in a partition file
• stats: Prints different characteristics of the alignment
  • alleles
  • alphabet
  • char
  • gaps
  • length
  • mutations
  • nalign
  • nseq
  • taxa
• subseq: Extract a subsequence from the alignment (coordinates on alignment reference or on a given sequence reference)
• subsites: Extract sites from the input alignment (coordinates on alignment reference or on a given sequence reference, or informative sites)
• subset: Take a subset of sequences from the input alignment
• sw: Aligns 2 sequences using Smith & Waterman algorithm
• translate: Translate input sequences/alignment (supports IUPAC code)
• transpose: Transpose 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

Goalign commandline 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 clustal alignment to fasta

goalign random --amino-acids --clustal --nb-seqs 2 | goalign reformat fasta --clustal

• 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

• Extract all sequences whose name starts with "mammal"

goalign subset -e '^mammal.*$' -i align.fasta

• Extract all sequences whose name does match the regexp

goalign subset -r -e '^mammal.*$' -i align.fasta

• Extract a sub sequences going from position 10 and with a length of 100

goalign subseq -i align.fasta -s 9 -l 10

• Compute a "logo" like consensus

goalign compute pssm -n 4 -i align.fasta

• Compute an evolutionary distance matrix (dna alignment only, 5 threads)

goalign compute distance -m k2p -i align.fasta -t 5

• Compute site entropry

goalign compute entropy -i align.fasta

• 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

Goalign api usage examples

• Parse a Phylip single alignment file and export it in Fasta

package main

import (
	"fmt"
	"os"

	"github.com/evolbioinfo/goalign/align"
	"github.com/evolbioinfo/goalign/io/fasta"
	"github.com/evolbioinfo/goalign/io/phylip"
)

func main() {
	var err error
	var f *os.File
	var align align.Alignment

	f, err = os.Open("f.phy")
	if err != nil {
		panic(err)
	}
	if align, err = phylip.NewParser(f).Parse(); err != nil {
		panic(err)
	} else {
		fmt.Println(fasta.WriteSequences(align))
	}
}

• Parse a Phylip multi alignments file and export it in Fasta

package main

import (
	"fmt"
	"os"

	"github.com/evolbioinfo/goalign/align"
	"github.com/evolbioinfo/goalign/io/fasta"
	"github.com/evolbioinfo/goalign/io/phylip"
)

func main() {
	var f *os.File
	var aligns chan align.Alignment
	var err error

	f, err = os.Open("f.phy")
	if err != nil {
		panic(err)
	}
	aligns = make(chan align.Alignment, 15)
	if err = phylip.NewParser(f).ParseMultiple(aligns); err != nil {
		panic(err)
	} else {
		for al := range aligns {
			fmt.Println(fasta.WriteSequences(al))
		}
	}
}

• Parse a Fasta file and export it in Nexus

package main

import (
	"fmt"
	"os"

	"github.com/evolbioinfo/goalign/align"
	"github.com/evolbioinfo/goalign/io/fasta"
	"github.com/evolbioinfo/goalign/io/nexus"
)

func main() {
	var f *os.File
	var align align.Alignment
	var err error

	f, err = os.Open("f.fasta")
	if err != nil {
		panic(err)
	}
	if align, err = fasta.NewParser(f).Parse(); err != nil {
		panic(err)
	} else {
		fmt.Println(nexus.WriteAlignment(align))
	}
}

• Parse a Fasta file and export it in Phylip

package main

import (
	"fmt"
	"os"

	"github.com/evolbioinfo/goalign/align"
	"github.com/evolbioinfo/goalign/io/fasta"
	"github.com/evolbioinfo/goalign/io/phylip"
)

func main() {
	var f *os.File
	var align align.Alignment
	var err error

	f, err = os.Open("f.fasta")
	if err != nil {
		panic(err)
	}
	if align, err = fasta.NewParser(f).Parse(); err != nil {
		panic(err)
	} else {
		fmt.Println(phylip.WriteAlignment(align, false))
	}
}

• Iterating over alignment sequences

	align.IterateChar(func(name string, sequence []uint8) {
		fmt.Printf("Sequence: %s\n", name)
	})

• Append identifier at the beginning of all sequence names

align.AppendSeqIdentifier("IDENT", false)

• Alignment statistics

var n int = align.NbSequences()
var l int = align.Length()

• Extract a sub alignment

var subalign align.Alignment
var err error
subalign,err = align.SubAlign(0, 100)

• Sort sequences by alphanumerical order

align.Sort()

• Copy/Clone the alignment

var clonealign align.Alignment
var err error
clonealign,err = align.Clone()

• Get the sequence having a specific name

var sequence string
var err error
sequence,err = align.GetSequence("nameofsequence")

• Build a bootstrap replicate

var bootstrap align.Alignment
bootstrap = align.BuildBootstrap()

• Randomly shuffle sequence order of alignment

align.ShuffleSequences()

• Compute evolutionary ditance matrix (5 threads)

import "github.com/evolbioinfo/goalign/distance"
//...
var model distance.DistModel
var distMatrix [][]float64
model = distance.Model("k2p", false)
distmatrix = distance.DistMatrix(align, nil, model, 5)

• Other functions

Other functions are described in the godoc.

Documentation

Overview

Main entry point for goalign command line