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Questions tagged [phylogeny]

Phylogeny is a statistical approach for reconstructing evolutionary relationships using trees

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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 ...
El Dude's user avatar
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2 votes
1 answer
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Why is my phylogenetic tree always splitting into one leaf and one node?

I used RAxML software on about 300 species mtDNA region (COI gene). Unfortunately I used a highly variable region so my tree only has highly support values for branches close to the leaves. But I also ...
Mirk's user avatar
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2 votes
1 answer
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How many ML tree should I build?

I created a phylogenetic tree of 328 species using RAxML. I run the ML algorithm 20 times and I chose the best tree (the one with the highest likelihood). The choice of 20 iterations was based on a ...
Mirko's user avatar
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0 answers
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Biopython PhyloTree to PyVis Network

We are trying to convert a Phylogenetic tree to networkx previously calculated with ...
El Dude's user avatar
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1 vote
1 answer
116 views

How to remove third codon positions from a charset in iqtree?

I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrate mitochondrial genes. These are my charsets: ...
Francesco De Giglio's user avatar
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0 answers
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Estimating rate of evolution from a phylogeny

Any suggestions for the best way to estimate a metric for evolutionary rate of viral sequences of the same species? I was using terminal branch length from a phylogeny and would quite like to try sub ...
Nitara Wijayatilake's user avatar
1 vote
1 answer
32 views

Confirming Identity of clone in Phylogeny

This might be something very trivial to ask, but I am new to this and was confused as in how to identify or differentiate between very closely related isolates from clonal isolate from the whole ...
prekij's user avatar
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3 votes
2 answers
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What is the best Query to retrieve DNA from NCBI?

I want to retrieve a sequence for many species from the Nucleotide database in NCBI. I'm using a command line approach and I have to figure out what is the best query that will return exclusively the ...
Mirko's user avatar
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1 answer
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Annotation result for phylogenetic analysis shows no common evolutionary gene in contigs, can i change the contigs?

I'm currently doing my thesis with the topic of phylogenetic analysis and is taking references from the previous person in my university (who have done the same topics but different species). They ...
Ayu Rani's user avatar
1 vote
1 answer
34 views

What happened to the PhyLoTA browser?

A paper I'm reading from 2021[1] mentions doing some analysis on data from the PhyLoTA database, with this reference citation: M. J. Sanderson et. al. 2008 The PhyLoTa Browser: processing GenBank for ...
Harry Richman's user avatar
4 votes
2 answers
162 views

How to create a phylogenetic tree from diverse mitochondrial genomes

I would like to create a phylogenetic tree for the most species in my dataset. I'm starting with around 1200 species, but since it's not good practice to align short and long sequences I tried ...
Mirko's user avatar
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1 vote
1 answer
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Error importing Maximum Credibility Tree from BEAST into R using treeio's read.beast()

I've encountered an issue that I'm hoping someone can help with. I constructed a phylogenetic tree using BEAST1 and then extracted the Maximum Credibility Tree using treeannotator. I'm trying to ...
Gerald Vasquez Aleman's user avatar
1 vote
1 answer
82 views

Approach for alignment-free phylogenetic tree generation using kmers

I have a general question about building phylogenetic trees without alignment: I want to build a tree using an alignment-free approach by counting kmers. I have found a lot of information in the ...
rimo's user avatar
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3 votes
1 answer
184 views

How can I convert my tree to the correct nexus format?

I would like to use the program BayesTraitV4. I have my phylogenetic tree in NEXUS format but the program does not accept it. I checked the example data and while they are also in NEXUS format, they ...
Nickmofoe's user avatar
  • 339
2 votes
1 answer
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Compare substitution matrices

I am looking for methods to compare substitution matrices to determine which one is better for a given set of data / type of protein. Do you know such methods / tools? e.g. BLOSUM62 vs PHAT for 50k - ...
maciejwww's user avatar
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1 vote
1 answer
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Genetic relationships between Cyanobacteria: terrestrial vs aquatic

I believe one of the site members is an expert in Cyanobacteria hence the question. I'm looking for a comprehensive 'phylogenetic tree' of the phylum Cyanobacteria and want to identify all the ...
M__'s user avatar
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1 vote
1 answer
71 views

Variation in 16S rRNA between assemblers - how do I know which is real?

I have a low-diversity metagenome (~11 bins > 80% completion). Out of the bins, 3 are of interest to me. None of the lower-completion bins that can be identified are from the group of interest. So ...
Laura's user avatar
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1 vote
1 answer
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phytools add.species.to.genus could not match your species to a genus

I have a species tree to which I am trying to add species, which includes a tip "Geissospermum laeve". When I run: ...
A. Bollans's user avatar
1 vote
1 answer
34 views

Finding linkage disequilibrium when I have a kinship matrix but not pedigree

I have a bunch of samples of a non-model organism divided in two groups: parental generation and offspring. I do not have a pedigree so I do not actually know who is a parent of who, and which are the ...
user1256923's user avatar
2 votes
1 answer
250 views

Correlation heatmap of RNA-seq clusters all samples together leading to very low no. of DEGs

I am writing to you to take an input or may be you can provide a different perspective. I am at wits end :( So I have nearly 200 samples. These are separated into two groups (group I treated with ...
Angelo's user avatar
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1 vote
1 answer
58 views

Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average

I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine... except some of the codon ...
Sudoh's user avatar
  • 217
2 votes
1 answer
69 views

How to determine the phylogeny of a specific set of genes

My goal is to understand the phylogeny of genes involved in bacterial restriction-modification systems, in psychrophilic bacteria. To do so here is what I have done. Downloaded the protein sequences ...
donkey's user avatar
  • 163
0 votes
1 answer
148 views

How to parallelize BEAST

I'm running BEAST v1.10.4 with BEAGLE v4.0.0. My dataset has one large partition and I have access to a machine with many CPUs so I would like to optimize performance by parallelizing the process. ...
flaszlok's user avatar
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1 vote
1 answer
305 views

How to add bootstrap values to the phylogenetic tree generated by OrthoFinder?

When we run the OrthoFinder analysis tool on a group of genomes to get the orthologues shared by them one of the output files include a folder named 'Species_Tree' that contains a text file named '...
K_081's user avatar
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1 vote
1 answer
92 views

Evolutionary tree from SNP data

I would like to make an evolutionary tree using the SNP data from DArTseq. Are there any software or packages available for this purpose? I came across the software SNphylo, but its home page is not ...
Lama's user avatar
  • 11
1 vote
1 answer
151 views

How to use Gblocks for trimming single-copy gene sequences?

I have run OrthoFinder on a set of 11 genomes and got the results in a folder. From the output folder, I saved all the single-copy gene sequences in a single FASTA file and now wish to remove all gaps ...
K_081's user avatar
  • 149
4 votes
1 answer
272 views

How to get a GISAID account? I registered months ago, still no reply!

Inspired by amateur variant hunters, I would like to join the Pango lineage proposal community and help contribute to variant surveillance. However, I cannot seem to get access to GISAID, the platform ...
AppleBees's user avatar
0 votes
1 answer
341 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__'s user avatar
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2 votes
1 answer
37 views

NCBI Blast databases - cannot find some databases

I'm working with a system that does local BLAST searches using some preconfigured BLAST databases. From what I see, these were updated within the last year, but I cannot find any current databases ...
KirkD-CO's user avatar
  • 175
0 votes
1 answer
229 views

Blast output file only shows 500 lines -outfmt 6

I had created databases of different sets of metagenome datasets - one with 6 runs, other with 48 runs, another with 100 runs, etc using the accession list for each of these datasets and makeblastdb ...
K_081's user avatar
  • 149
1 vote
0 answers
60 views

How to identify all descendents of a branch on a phylogeny

I'm trying to simulate the evolution of binary traits on phylogenies in R to end up with a dataset of the traits held by each tip. Starting at the root, at every timestep, new traits are added with a ...
Daniel Pelletier's user avatar
3 votes
1 answer
108 views

What is the limit of partition incompleteness in Bayesian MCMC?

I am seeking advice on whether or not to incorporate incomplete data into my BEAST analysis. I have HIV data consisting of two partitions of the pol gene: one that is 1.2 kb in length and present in ...
Vovin's user avatar
  • 435
2 votes
1 answer
48 views

Parsimony-distance neighborhoods in tree space

I have the following question about the paper A parsimony-based metric for phylogenetic trees by V. Moulton and T. Wu. In this paper, the authors define a "parsimony-distance" between ...
Harry Richman's user avatar
3 votes
1 answer
67 views

compare fasta sequences in pairs and collect metrics

I have 96 fasta files (A1, A2, A3...) from one plasmid assembly pipeline, and I have another 96 fasta files (B1, B2, B3 ...) from another plasmid assembly pipeline. I would like to compare pair ...
cautree's user avatar
  • 139
2 votes
1 answer
63 views

Using ticks on the x axis or a scale bar when visualisizing a phylogram?

When visuliazing a phylogram is it preferable to show ticks on the x axis or a scale bar? Given an example tree with branch lengths in newick format ...
Tony's user avatar
  • 43
0 votes
1 answer
120 views

Calculating total number of Unique gene in every genome from ROARY pangenome output

I performed a ROARY from 100 genome. I got several file including gene_presence_absence.csv from the results. I want to know how many unique gene(unshared gene, based on blast homology, same gene (...
Umar's user avatar
  • 135
3 votes
1 answer
266 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 ...
helle's user avatar
  • 33
2 votes
1 answer
144 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: ...
rimo's user avatar
  • 1,003
2 votes
1 answer
81 views

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 ...
Laura's user avatar
  • 937
3 votes
1 answer
90 views

Why is COI metabarcoding not used for prokaryotes?

I'm a beginner in bioinformatics working with environmental metabarcoding, and while reading up on different marker genes, I understand that COI is preferably used for animals thanks to its higher ...
Joel's user avatar
  • 55
1 vote
1 answer
117 views

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 ...
I Del Toro's user avatar
2 votes
1 answer
45 views

Should I compensate for two clusters of samples in microarray by hierarchical clustering and MDS?

I seem to have two groups of samples based on hierarchical clustering as well as MDS plot analysis using the sample label from the tree cut of the hierarchial clustering. I am analyzing microarray ...
siddhartha das's user avatar
2 votes
1 answer
65 views

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 ...
Sudoh's user avatar
  • 217
2 votes
1 answer
112 views

What do you use the CLANS program for?

I am reading this paper called Birth and death in the Terminal Complement pathway, doi : https://doi.org/10.1101/2022.04.21.489004 where they have performed CLANS analysis. I understand that CLANS ...
venkatesh war's user avatar
2 votes
1 answer
80 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 ...
Nickmofoe's user avatar
  • 339
3 votes
2 answers
114 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) ...
Nickmofoe's user avatar
  • 339
1 vote
1 answer
55 views

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!
Balint Biro's user avatar
2 votes
1 answer
76 views

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 ...
Adi's user avatar
  • 21
1 vote
1 answer
91 views

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 ...
DataScienceNovice's user avatar
1 vote
1 answer
55 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 ...
Gerald Vasquez Aleman's user avatar

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