All Questions
37 questions
3
votes
2
answers
97
views
Biopython / ETE3 get subtree of a newick tree
I can not find a good example how to extract a subtree from a phylogenetic tree with either library.
I can load newick files etc, but not sure how to search for a ...
- 195
1
vote
0
answers
25
views
Biopython PhyloTree to PyVis Network
We are trying to convert a Phylogenetic tree to networkx previously calculated with
...
- 195
0
votes
1
answer
475
views
Refactoring pandas using an iterator via chunksize
This question was also asked on Stack Overflow
Bioinformatics rationale eggNOG files can be very big and sump all available RAM for regular to medium sized desktops.
I am looking for advice on using ...
M__♦
- 13k
3
votes
1
answer
304
views
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 ...
- 33
2
votes
1
answer
184
views
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:
...
- 1,063
2
votes
1
answer
515
views
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 ...
M__♦
- 13k
3
votes
1
answer
162
views
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 ...
- 33
1
vote
2
answers
139
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?
- 11
1
vote
2
answers
59
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. ...
M__♦
- 13k
1
vote
1
answer
386
views
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 ...
- 141
0
votes
2
answers
1k
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.
...
- 141
3
votes
1
answer
118
views
Missing ',' in line when Biopython reads a nexus tree
I want to edit a tree that I got from BEAST2 treeannotator in nexus-format.
Usually I use the module Phylo from Biopython for such work but ...
- 435
1
vote
2
answers
143
views
Bio.codonalign.codonseq module (cal_dn_ds) for SARS-COV-2
I have calculated the dN,dS ratio for a SARS-COV-2 data set ('NC_045512.2' (Wuhan strain) and 'LC666924.1'), and results in a zero value (for most of the genes).
Is it possible and what is the ...
- 11
1
vote
2
answers
311
views
Permutations of 4 amino acid sequence oligopeptide
I have an assignment for a project to build a tetrapeptides library to screen against some target enzymes in silicon.
I am looking for a script to construct about 160000 tetrapeptide from the 20Amino ...
- 23
2
votes
2
answers
199
views
Create a NHX phylogeny format with r or python
I need help to add information in my phylogenetic tree on each branch.
I have two pieces of information at my disposal:
A phylogenetic tree in newick format :
(mammal:0.14,turtle:0.02,(rayfinfish:0....
- 199
2
votes
1
answer
517
views
How to extract clusters from a phylogenetic tree?
I am using Biopython Phylo and RDkit Cluster to obtain a UPGMA tree from a distance matrix of 5k x 5k entries. How can I extract the taxa names within a given clade(s)?
For example, Bio.Phylo can ...
0
votes
2
answers
59
views
How to obtain desired output?
I am working on a project using the following command within nano:
...
0
votes
2
answers
147
views
How to fix NameError?
I am working on a project and am having issues with the following code that I have written in nano:
...
1
vote
1
answer
698
views
Why SeqIO.parse method isn't working?
I am trying to follow the tutorial from from the Biopython website here and I am right at the beginning (2.4.1), where I am trying a Simple FASTA parsing example which is
...
2
votes
2
answers
40
views
Any suggestions for cultivar identification using SSR (simple sequence repeat) markers
This is the data I have now: 30 simple sequence repeat (SSR) markers for 80 cultivars of cucumber. 10 of the 80 cultivars belong to one cultivar (let's say A).
My goal is to classify an unknown ...
- 121
1
vote
1
answer
271
views
Phylogenetics software that can represent collapsed nodes as triangles
I am trying to represent a large (100-300+ sequences) phylogenetic tree in a way that gets my point across. I figured that reducing the number of branches (by collapsing clades which include highly ...
- 1,027
1
vote
2
answers
2k
views
How to create a .phy file for constructing a phylogenetic tree?
I'm new here. I need to construct a phylogenetic tree from 16s Sequence data (merged 151 bp) and color the branches/nodes based on my experimental conditions. From this blog, it looks like I need a ....
- 11
0
votes
1
answer
2k
views
How to generate ultrametric phylogenetic trees?
This question has also been asked on Biostars
I am going to use ultrametric tree for downstream analysis. I would like to see use the ultrametric tree for Ranger-DTL for infer gene family evolution by ...
- 109
3
votes
2
answers
920
views
PDB file downloading: pymol automation vs. manual
I automated a PDB download using a Pymol script (below)
...
M__♦
- 13k
3
votes
2
answers
1k
views
How to find common sequences among 6 multi-fasta files
I have 6 multi-fasta files, every of them contains ca 1500 sequences like that:
...
- 41
1
vote
1
answer
152
views
Pandas automatically rounds GWAS P-value
I am working with a specific GWAS. If I were to run this on the command line
grep <rs_id_of_interest> GWAS.txt
I would see the GWAS p-value to be on the ...
- 113
1
vote
1
answer
374
views
What do negative dN or dS mean in cal_dn_ds in Biopython?
I'm noobie in bioinformatics. I use cal_dn_ds from Bio.codonalign.codonseq with method 'NG86'. Sometimes I get dS=-1. What does ...
- 113
1
vote
1
answer
59
views
How to allow "half windows" in biopython?
I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window ...
- 409
7
votes
5
answers
7k
views
How to create Phylogenetic Trees from fasta files in Python or R?
I have around a hundred Fasta files (and will collect several thousand) with DNA sequences and +50x coverage. What is a recommended method to construct a phylogenetic tree? Solutions in Python or R ...
- 1,305
3
votes
2
answers
5k
views
Python - Finding a motif - input: a txt file with 10 sequences and 10 motifs
When I run my BruteForce function with only one input it works and the result is correct.
...
- 31
2
votes
0
answers
325
views
How to get bootstrap support of phylogenetic tree?
I have used multiple sequences aligned file of protein data to generate a maximum parsimony tree, then I used the "bootstrap_trees(msa, times, tree_constructor)" ...
- 503
7
votes
2
answers
813
views
Truncating branch length values of Phylogenetic tree with biopython
I have been using biopython 1.72 to display my phylogenetic tree files.
Using the function 'Phylo.draw(pars_tree, branch_labels=lambda c: c.branch_length)' to ...
- 503
5
votes
2
answers
312
views
How to plot character state changes from a presence-absence matrix on to a phylogeny
I wish to assign character state changes from a presence-absence matrix to a phylogeny. Thus I want to identify the most parsimonious hypothesis for which node and branch a given "mutation" or "change"...
- 151
5
votes
2
answers
163
views
Counting letters in phylip alignment columns with Biopython
I have been using python 3.6 and biopython 1.72 to work with protein data files. I am using a protein sequence file (phylip format), for example:
...
- 503
3
votes
1
answer
275
views
How to assess the quality of assembled .fasta genome files?
I have assembled 3 .fasta files from contigs infastq format of 3 different Homo sapiens.
I would like to see if the assembled ...
- 1,447
3
votes
1
answer
564
views
Issues installing Dendropy
I want to perform phylogenetic analysis using Dendropy. I have installed dendropy using command sudo pip install -U dendropy but when I import it in python3.5.1 it ...
5
votes
1
answer
466
views
How to find which scales are available in SeqUtil of Biopython?
I am trying to analyse the hydrophobicity of a sequence using BioPython's "SeqUtil".
...
- 409