Questions tagged [phylogenetics]

Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.

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Plot phylogenetic tree from list of edges

I have a dataset that I wish to convert to tree or phylo format like in the ape package, in order to plot the phylogenetic tree. It is formatted like a list of ...
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eggNOG API, how's it work?

Background eggNOG uses seed orthologues which correspond to its own internal database, so for example J421_1876 can be placed in its online search engine here. This ...
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2 votes
1 answer
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Math on Pandas Columns

I have a pandas dataframe that reads in a PAF file from minimap2. What I would like to do is take the first 5 columns of the data from to create a BED file. I used this to extract the first 5 columns: ...
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2 votes
1 answer
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Is there a graphical/interactive 16S rRNA clustering method?

I've been doing phylogenetics with large (hundreds) 16S rRNA sequences lately. Usually I'm focusing on one order, and using a combination of trees and sequence similarity to assess stuff like 'is this ...
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1 vote
1 answer
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Phylogeny building in R from FASTA files:

Im working on building a phylogeny from scratch with downloaded FASTA sequences from GeneBank. I think Im doing alright up until the multi sequence alignment in the ...
2 votes
1 answer
45 views

Is there a way to calculate the number of parsimony informative characters in a morphological dataset in R?

I have a dataset of binary morphological characters and would like to know how many of them are parsimony informative. Is there a way to calculate this with an R package?
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2 votes
1 answer
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Is it possible to do homology inference across species using different kinds of NGS data?

Background: I have a list of species that I want to put through homology inference. The goal of homology inference is to investigate the evolution of a trait on a species tree. I want to use the ...
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3 votes
1 answer
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Is there a way I can combine geological data with population genetics data?

So I have ran SAMOVA and made calculations regarding haplotype diversity and nucleotide diversity of several populations. I have also made raster data regarding geographical data like slope, ...
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2 votes
1 answer
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Using R `ggtree`, attach extra data next to the nodes on an illustrated tree/newick file

This is really a programming question but ggtree might be too obscure for this question to be posted on StackOverFlow as a general R related question. I am having ...
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Where can I find the FCT value after running samova?

I have ran SAMOVA 2.0 for 2 groups so far. I want to determine the right number of groups and I know that the correct way is to run it more than once with a different amount of groups and then check ...
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3 votes
3 answers
108 views

Read Clustal file in Python

This question was also asked on StackOverflow I have a multiple sequence alignment (MSA) file derived from mafft in clustal format which I want to import into Python and save into a PDF file. I need ...
2 votes
1 answer
55 views

How can I fix "Ill-defined genetic structure" Error message in Arlequin?

I am performing an AMOVA analysis via Arlequin. At this point, I have: collected sequences of mtDNA from the cox1 gene, aligned the different genes using clustalX converted the files into .arp ...
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1 vote
1 answer
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How can I use sequences with different lengths in arlequin?

I have mtDNA sequences of the cox1 gene from various populations of one species. I want to perform an AMOVA allele frequency analysis via Arlequin. This allele frequency package however requires my ...
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3 votes
2 answers
79 views

How can I resolve "missing name of population" message in PGDSpider?

I want to use Arlequin for AMOVA. I have my FASTA files which I want to convert into .arp files which are recognizable by arlequin. When I try to convert it using Population Genetics Data (format) ...
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1 answer
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DNA, molecular descriptors

Are there any programs (preferably command line tools) for calculating molecular descriptors of DNA? I am looking for something like Chemopy or RDKit but specifically for DNA. Thanks in advance!
2 votes
1 answer
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How to make unrooted tree for Likelihood mapping result by using IQ2-tree?

I am a biologist, and I do not fully understand the tree topology of the experimental species. I used four-taxon set (4 sequences) to identify the Four-cluster Likelihood-Mapping by using ...
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3 votes
1 answer
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Downloading genes from NCBI in fasta format

I'm pretty new in bioinformatics. I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I'd rather do this through via code than download ...
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1 vote
1 answer
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Maximum likelihood estimation for tree construction

Could someone direct me to a resource (textbook chapter, lecture notes, online video, etc.) that demonstrates, in a mathematically or computationally rigorous way, how to use maximum likelihood ...
1 vote
0 answers
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segmasker doubles found intervals

During NCBI BLAST+ segmasker output exploration, I found out that for some sequences, the program returns the same interval twice: ...
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2 votes
0 answers
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Why does segmasker modify headers?

When parsing NCBI BLAST+ segmasker output, I realized the program modifies almost every header containing these strings: ( or )...
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2 votes
2 answers
160 views

How to wget a gff from NCBI database?

Say I want to use wget to download a gff file for the X chromosome of release 5.57 of the Drosophila melanogaster genome. The NCBI page with the gff file for just this is here. However, I do not see ...
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1 answer
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finding the frequency of a motif-matching peptide

This question has also been asked on Biostars I want to find the frequency of each motif-matching peptide. The sequences are: ...
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1 vote
1 answer
51 views

How to identify mutations in a viral genome

I have a fasta file with multiple sequences comprising 38 sequences. The length of the sequences are around 11000 bp. How can i get changes in the genomes based in a reference genome? (aa subtitutions ...
1 vote
0 answers
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ETE4 manual or improved code description

ETE3 * (Environment for Tree Exploration) is a major package and in particular Python package to navigate phylogenetic trees. It is the premier coding library/package for tree manipulation. ETE4.0.0 ...
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2 votes
1 answer
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Converting Pairwise single- linkage clustering distance data to "newick" format

I have pairwise distance data for single linkage cluster and I would like to convert it to newick format. I was unable to find a conversion algorithm. I require newick format for visualization and ...
3 votes
1 answer
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Compare and Reorganize Fasta Headers Python

I want to compare the headers from the fasta file to file1, and if there's a match, reorganize the header and put the match first. If there's no match between fasta file and file1, look at file2 and ...
1 vote
1 answer
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Using information criteria weights to create consensus tree

While I am familiar with calculating information criteria for various ml models of a multiple sequence alignment, I am not aware of how to use the derived weights to create a tree that combines ...
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2 answers
81 views

How can I align two novel sequences to a reference genome and build a phylogenetic tree?

I have two new amino acid gene sequences that I want to align to a reference genome. Is it a good idea to have a combined phylogenetic tree? what will this type phylogenetic analysis called?
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2 votes
1 answer
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How do I generate a variant list using Illumina reads from a Salmonella genome?

I am planning on performing phylogenetic analysis of Salmonella specimens using WGS data from PulseNet and GenomeTrakr, for the purpose of public health surveillance & to provide context for ...
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1 vote
1 answer
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How to get full headers with tabs as separators with segmasker?

I try to pass a .fasta file with headers where tabs are used as separators as input file to NCBI BLAST+ segmasker: ...
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2 votes
2 answers
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Add file name to FASTA file header using SeqIO

I have several fasta files that represent the proteins from different orthogroups. However, the orthogroup that each of the proteins belongs to is not indicated within the files. I am leveraging ...
1 vote
1 answer
23 views

Retrieval protein definition from accession ID

I have a list of protein accessions: XP_025107904.1 PVD22034.1 AJA37836.1 How can I obtain the definition of the protein, and the related organism? Output: ...
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4 votes
1 answer
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How to promote assemblies into genomes in NCBI?

Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed. I'm working with Drosophila subobscura. (spring fruit fly) I see here https://www.ncbi.nlm.nih.gov/data-...
1 vote
2 answers
79 views

How to merge multiple list into a single dataframe replacing common values with 1 -python

I have multiple lists on python: ...
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1 vote
0 answers
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I want to map TFBS on to the sequences from dataset containing 8448 (210 base) sequences. its not giving all the hits I need

I want to map TFBS (transcription factor binding sites) on to the sequences from dataset containing 8448 (210 base) sequences, but it is not giving all the hits I need ...
0 votes
1 answer
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Single or partitioned model for supermatrix tree inference?

I am dealing with several genes in my dataset. For each of the genes, I have built gene tree, with their best estimated model. I am intended to look into the effect of the tree from concatenated ...
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1 vote
1 answer
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Fixing FASTA file for Local BLAST Database

I recently prefetched 157 SRA files from an NCBI BioProject using the SRAtoolkit. I then used the toolkit to download those files in FASTA format. Each individual FASTA file looks something like this: ...
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3 votes
1 answer
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How does one distinguish nuclear DNA from mitochondrial DNA when doing WGS?

I'm interested in doing de-novo sequencing but also phylogenetic analysis. In particular, after de-novo sequencing and annotating the genome, I need to align the CO1 gene and the nuclear 28S rRNA gene ...
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2 votes
1 answer
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drawing multiple sequence alignment as tree in R

I am very new here. Please help me with my codes as am trying to draw multiple sequence alignment as tree suing ggtree package in R and i have following error. ...
1 vote
1 answer
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CLI access to genomes/proteomes by BioSample ID [duplicate]

This question was also asked on Biostars I'd like to download multiple genome assemblies or proteomes using a set of BioSample IDs from NCBI. I'm able to find the assemblies belonging to the BioSample ...
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1 vote
0 answers
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Is there a DNAWeaver How-to guide?

Recently I've been trying to use DNA Weaver for customized gene assembly design. Although there is a web version that allows to perform some assembly examples, I've tried to replicate them with python ...
3 votes
0 answers
30 views

How are BLAST record scores calculated in biopython

Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is ...
1 vote
2 answers
53 views

Improving list speed: glycosylation example

I discussed a question with @gaspanic Python/Biopython - Replace amino acid residue on MSA with "z" from a list of unaligned positions . The issue emerged was speeding up lists in Python. ...
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1 vote
1 answer
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reverse translation from amino acid string to DNA strings

what is the opposite of .translate() function calls ? I mean let's say I am given an amino acid string CYCLIC, how do I obtain all the possible combinations of DNA ...
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2 answers
438 views

RNA strings and amino acid string

Which of the following RNA strings could translate into the amino acid string PRTEIN? (Select all that apply.) I am not sure if the following mass of amino acid is relevant to the question. ...
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2 votes
1 answer
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Parsing text within a taxonomy.csv file

I have the following file in tab separated values (TSV). ID Taxonomy 76980f6d906c6baaef3f96559fc7ba1b d__Eukaryota; p__Cercozoa; c__Vampyrellidae; o__Vampyrellidae; f__Vampyrellidae; g__uncultured ...
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Calculate interval of flanking introns

I am looking for a easy way to calculate the intervals of flanking introns based on a transcript annotation file. I have chosen a very complicated method: ...
1 vote
1 answer
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PCA analysis of samples in a phylogenetic tree

I have a phylogenetic tree. Each branch ends have samples (s1, s2, ~ s16). What I want to do is, I want to make PCA analysis plot for each sample. First I thought each sample has each lineage (...
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1 vote
3 answers
495 views

How can I remove FASTA sequences with an asterisk inside the sequence?

I have several protein sequences with an asterisk in the middle of the sequence, and I'd like to remove those sequences. In the example below, I have three sequences: From this example, I would like ...
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3 votes
2 answers
485 views

R ggtree apply colors to branches with multiple colors

This question was also asked on StackOverflow I have a phylogenetic tree made with a Newick format ((a:1,b:1):2, (c:1, d:1):3):1; The output will be I have drawn ...
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