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Questions tagged [clustal]

Clustal is a set of tools for multiple alignment of nucleic acid and protein sequences.

Clustal2

Clustal2 has two versions: ClustalW presents a command-line interface, and ClustalX provides a GUI.

Clustal Omega

Clustal Omega, or clustalo, is the latest version of Clustal. It employs a new HMM alignment engine, resulting in greater accuracy. Clustal Omega is currently in beta, with a command-line interface and web server version only.

A full description of the algorithms used by Clustal Omega is available in Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

Web services

All Clustal products have web server versions that can be accessed at www.clustal.org.

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BioPython, how to convert from .fasta to .aln for clustal alignment?

I've a .fasta file that I wish to convert to .aln so that it can be aligned with the alignIO.read command or somehow give my fasta file "Clustal Headers" because when I use the fasta file it just outputs that it's not a known clustal header, is the…
tan
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phylogenetic trees from nucleic acid words

If for n nucleic acid sequences a table of word frequencies (the sequence ATG corresponds to two words of length 2, AT and TG) is constructed, then that table can be used (directly or after dimensionality-reduction by PCA) to calculate a distance…
Engelbert Buxbaum
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Running clustalw on google platform with error in generating .aln file in ubuntu

I was trying to run clustalw from Biopython library of python3 on Google Cloud Platform, then generate a phylogenetic tree from the .dnd file using the Phylo library. The code was running perfectly with no error on my local system. However, when it…
Hang Lin
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I get an error when execution the function clustal() in r

I am beginner R and I try to run the command clustal(sylvia.seq) I get the following error: sh: clustalw2: command not found Error in clustal(sylvia.seq) : cannot find executable ‘clustalw2’ on your computer. It is recommended that you place…
Chicago1988
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Can't run Clustalw through Bioperl

I m trying to run the script below. but I get the error: ------------- EXCEPTION ------------- MSG: Cannot find executable for clustalw. path="clustalw.exe" STACK Bio::Tools::Run::WrapperBase::executable C:/Perl64/site/lib/Bio/Tools/Run/…
Dimitri C
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Error in Bioperl program execution

I have installed bioperl but confused where to get it and where to run the bioperl program.Then I have tested for it and it was successful I have run a program for multiple seq. alignment. Generated an error Can't locate…
Rajkishore90
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Run clustalw2 without input FASTA file

how can I run ClustalW2 without a input FASTA file? Can I add a pipe to the command? I am currently following section 6.2.1 in the Biopython Tutorial and Cookbook.
El Dude
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read.alignment from seqinr adds new line characters

I stumbled upon a weird behavior of the read.alignment function from the seqinr R package when reading in a Clustal Omega output file. The function doesn't seem to be able to properly parse the input. Consider this as a test.clu file: CLUSTAL…
Marius
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'numpy.float64' object does not support item assignment alignment sequences

I am developing a program to calculate the sp scores of aligned sequences from the Percent Identity Matrix obtained on Clustal Omega. I have problems with element casting in python. I'm trying to store the values read from a text file in an array of…
cs1234
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writing FASTA file output in R

I am trying to perform Multiple Sequence Alignment using ClustalW. The code works, and I am able to see the alignments on my terminal in R. Below is the code that I wrote. library(BiocManager) library(msa) library(Biostrings) mySequences <-…
thole
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R package immunarch can't find clustal w

everyone. I am trying to use a R package 'immunarch'. In one of its main function repAlignLineage, clustal w needs to installed to do the alignment. However, after install clustal w2 in my windows 11 system, r studio still shows erro message. How to…
user2953619
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How to use MSA and Clustal for python inside a Jupyter notebook?

I have a FASTA file with sequences associated with states and their cites. Is it possible to use python through Jupyter notebook to run a MSA and clustal, then create a phylogenetic tree with the align sequence. I am not sure where to start and…
rt2421
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Biopython Alignment using Muscle or ClustalW without file input

I'm actually building a script in python3 to calculate divergence between several paired sequences. So, I need firt to make an alignment between 2 proteines sequences and then make a codon alignment with 2 dna sequences. To make my first alignment…
Grendel
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Print 50 sequences from each line using Clustal

I have a multiple sequence alignment (Clustal) file and I want to read this file and arrange sequences in such a way that it looks more clear and precise in order. I am doing this from Biopython using an AlignIO object: alignment =…
MysticCodes
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Terminals being renamed None with Biopython Phylo

I have been using Biopython to align some amino acid sequences with Clustal-Omega, then import the tree generated. from Bio.Align.Applications import ClustalOmegaCommandline from Bio import AlignIO from Bio import Phylo clustalomega_cline =…
jargogler
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