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Read Clustal file in Python

pyMSAviz may help with this problem. pyMSAviz is a Python tool with a convenient CLI/API implementation for visualizing MSA files. For example, you can output MSA figure in PDF format with the ...
moshi's user avatar
  • 31
3 votes

Remove gaps from alignment?

You may also find useful the BMGE tool (stands for Block Mapping and Gathering with Entropy). BMGE selects regions in a multiple sequence alignment that are suitable for phylogenetic inference by ...
Stas Malavin's user avatar
3 votes
Accepted

File format of substitution matrix in clustalw

This example seems to have information on this, looks like it should have this format: ...
Bioinfomrat's user avatar
2 votes

Multiple Alignment cost application

I'm not a fan personally, but it is context specific. The problem is that it is heading towards optimisation, particularly algorithmic optimisation. If the alignment is the final calculation - that is ...
M__'s user avatar
  • 12.5k
2 votes

find conservative regions relative to a specific accession

You can opt for a similarity matrix as output (here is an example). The fact that you would like to judge conservation "relative to a given sequence", you can use this matrix to rank ...
haci's user avatar
  • 4,142
2 votes

ClustalOmega alignment

Have you had a look at your alignment? I personally use Jalview but any alignment viewer should work. Colour > Percentage Identity (or Nucleotide) should help with visualization. Does the alignment ...
Laura's user avatar
  • 909
2 votes

Select representetive sequence within MSA (protein)

I have two suggestions that I used in the past (both using Python/BioPython though). They are arguably the same, but obtained through different paths. Calculate the (artificial) consensus sequence of ...
albertr's user avatar
  • 71
2 votes

multi-sequence alignment of samples with multiple contigs each

in the end, I just loaded the .bam files into artemis and, by inspecting the depth (heat-map), I could check which samples had the genes I was looking for:
BCArg's user avatar
  • 283
2 votes

multi-sequence alignment of samples with multiple contigs each

If you have a reference genome (or are willing to designate one of your de novo assemblies a reference), you may find QUAST helpful. QUAST will perform an alignment of all genomes against the ...
Maximilian Press's user avatar
2 votes

multi-sequence alignment of samples with multiple contigs each

MUMmer4 is a versatile alignment tool for DNA and protein sequences. It supports one reference genome and up to 32 query genomes. MUMmer4 will align every contig in each genome to the reference genome....
Forrest Vigor's user avatar
2 votes
Accepted

Read Clustal file in Python

Ok, figured out a way, not sure its the best one, nedd to install fpdf2 (pip install fpdf2) ...
pippo1980's user avatar
  • 1,088
2 votes
Accepted

How to identify sequence origin in DNA shuffle reads?

This is the sort of thing that LAST has been specifically designed to work well for: LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially good at finding ...
gringer's user avatar
  • 14.2k
2 votes

Remove gaps from alignment?

If you want an ungapped alignment, you could do an ungapped alignment (the older read aligners were ungapped, e.g. bowtie). However, I suggest that you don't want an ungapped alignment, you just want ...
Chris_Rands's user avatar
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2 votes
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How do I plot clusters based on DNA sequence alignment?

I think one of the reasons you struggle is that clustering DNA sequences is not a clearly defined task. In general intention of clustering is to reconstruct, or approximate the relatidness of the DNA ...
Kamil S Jaron's user avatar
2 votes

Read Clustal file in Python

adding, a second answer because the OP request about I need to import the file and then highlight some specific word was making me uneasy. I kept using the Pyfpdf2...
pippo1980's user avatar
  • 1,088
2 votes

How to create a phylogenetic tree from diverse mitochondrial genomes

It looks like these are random mitochondrial sequences pulled from NCBI, which is probably why the alignments aren't working well. As a starting point, I recommend you make sure that all the ...
gringer's user avatar
  • 14.2k
2 votes
Accepted

How to create a phylogenetic tree from diverse mitochondrial genomes

Your overall approach is cool, given caveats (below) to adapt the method. I can fairly authoritatively say your specific methodological approach will not work regarding its phylogenetic strategy ...
M__'s user avatar
  • 12.5k
2 votes

Current 'most comprehensive' whole genome alignment resource for human?

The obvious thing missing from your list is the telomere-to-telomere genome assemblies that have been coming out in the last couple years. Assembly link here. There are now a few others as well that ...
Maximilian Press's user avatar
2 votes
Accepted

BioPython bootstrap is not reliable?

I think this is a bug. It seems to work if you do this, creating an equivalent Alignment object instead of a MultipleSeqAlignment to give the bootstrap step: ...
Jesse's user avatar
  • 947
1 vote

How to highlight the specific peptide sequences after performing multiple sequence alignment for the fasta file?

Checkout an MSA visualisation and analysis package that you can load the alignment into. It may not be the newest tool, but I've used Jalview (https://www.jalview.org/) in the past
Chris_Rands's user avatar
  • 3,948
1 vote

drawing multiple sequence alignment as tree in R

Firstly, do check tree is not an empty object, i.e. it uploads the tree file. Secondly, check the path to the alignment is correct ...
M__'s user avatar
  • 12.5k
1 vote

multi-sequence alignment of samples with multiple contigs each

It won't work on more than 3 genomes at a time, but SynMap3D from the Comparative Genomics webserver (https://genomevolution.org/coge/) should do the trick. I'm mentioning it here because the ...
Laura's user avatar
  • 909
1 vote

Generate consensus protein sequence from relatively gappy alignment?

Given the alignment you've presented, there are obvious groups of sequence similarity, but I'm seeing a lot of different peptide sequences in this (e.g. ...
gringer's user avatar
  • 14.2k
1 vote
Accepted

Sequence alignment with MUSCLE

HMM Super5 is a hidden Markov model (HMM) where gap penalties and the substitution matrix are the parameters at the centre of the model. That is the answer, thats why you can't change it - it does it ...
M__'s user avatar
  • 12.5k
1 vote

How to make MSA for contact prediction?

You might have some luck with Parsnp. From the description: Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be ...
Throckmorton's user avatar
1 vote

How to make MSA for contact prediction?

That's a LOT of sequences! I'm doubtful you'd be able to get TripletRes or CCMPred to run at all with an MSA depth of 1.5 million. I suggest pruning your dataset to remove redundant sequences (...
jhschwartz's user avatar
1 vote

Remove gaps from alignment?

This new tool, CIAlign, talks about some automated removal of gaps in multiple sequence alignments https://twitter.com/thekatybrown1/status/1306215132670889984 https://github.com/KatyBrown/CIAlign
Colin D's user avatar
  • 186
1 vote

Remove gaps from alignment?

Gblocks is a tool for removing gaps/poorly conserved positions from alignments. Available here. Here is a webserver that runs it for you. It's a bit old, possibly there are others at this point.
Maximilian Press's user avatar
1 vote

BEAUti not accepting taxa tip dates

I found the solution, one of my Seq IDs had a , in one of the meta-data fields, this appears to have thrown off the software and all subsequent Seq IDs could not be ...
MicroBiostat's user avatar

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