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Questions tagged [phylogenetics]

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

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4 answers
2k views

Retrieving NCBI Taxa IDs from refseq or GenBank assembly accession

I have about 10,000 genome files all named by either refseq or genbank accession number, do you know if it's possible to convert these numbers to the corresponding NCBI taxon ID or species? for ...
1 vote
1 answer
108 views

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 ...
5 votes
1 answer
237 views

UPGMA computation

The unweighted pair group method with arithmetic mean (UPGMA) is a hierarchical clustering method, for example used in phylogeny. In a phylogenetic tree it would result in a global molecular clock ...
1 vote
1 answer
84 views

Selection analysis based on each leaves as foreground with FastCodeML

I am using positive selection analysis for each leaves in a phylogenetic tree. In the routine calculation via codeml, I will be running model zero for all leaves ...
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 ...
0 votes
1 answer
74 views

Scale on the y-axis in a tree rotated with 'layout_dendrogram()' using ggtree

I'm editing a time-scaled tree using ggtree. The dates are correctly adjusted when I apply the 'mrsd' command and 'theme_tree2()', but when I try to rotate the tree with 'layout_dendrogram()', the ...
3 votes
2 answers
884 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
1 vote
1 answer
135 views

Select synonymous sites from a multiple sequence alignment

Could someone kindly recommend a tool or R package that can identify synonymous sites in a multiple sequence alignment? I wish to select those taxa for tree reconstruction and other downstream ...
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: ...
1 vote
1 answer
44 views

Arbovirus phylogenetic analysis using the BEAST2 software via a global clock model

How do I perform a global clock phylogenetic analysis of an arbovirus using the BEAST2 software. If I intend to utilize the global clock model for analysis, kindly guide how to set the parameters of ...
3 votes
2 answers
42 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 ...
2 votes
1 answer
254 views

Merging ssu-align alignments

ssu-align is an HMM-based MSA tool for ribosome's small subunit (SSU) sequences. It's bundled with three SSU models: archaeal, bacterial eukaryotic Approach Given a set of archaeal and ...
1 vote
1 answer
146 views

Problem with classification model of genomic data: every machine learing model predicts wrongly almost always the same subset of dataset

First of all, I'd like to apologize for any spelling or grammar mistakes. I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
3 votes
2 answers
466 views

Can't load files into PopART

I am trying to create haplotype networks in PopART (Population genetics with Reticulated Trees*) which I have successfully done many times in the past. Two weeks ago the program was working fine for ...
1 vote
1 answer
60 views

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 ...
2 votes
1 answer
18 views

How to interpret high support values for terminal nodes and low for more ancient nodes?

I made a phylogenetic tree for about 300 species using a region of the COX1 gene. The tree looks visually meaningful: species of the same genus are all clustered together. Then I performed a 350-...
1 vote
1 answer
123 views

Problem with setting fixed topology for MrBayes

I need to use partitioned DNA input (concatenated multiple genes) and fixed topology (species tree from ASTRAL) to get branch lengths in MrBayes. I have input NEXUS like: ...
3 votes
1 answer
56 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 ...
2 votes
1 answer
28 views

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 ...
5 votes
1 answer
2k views

How to install DnaSP on a Mac

I need to install DnaSp, a nice GUI originally written for Windows for the population genetics of nucleotide sequence data. However, its not working on my mac. I'm using wine to install it using these ...
1 vote
1 answer
137 views

How can extract the list of genes name from the raw data in GEO?

The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R? I would ...
2 votes
1 answer
102 views

Build tree to calculate beta diversity

I am trying to calculate beta diversity* using the UniFrac distance on my data, each sample having OTUs values. To calculate it, I saw it required building a tree with percentages that represented the ...
1 vote
1 answer
41 views

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 ...
2 votes
1 answer
37 views

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 ...
1 vote
0 answers
22 views

Biopython PhyloTree to PyVis Network

We are trying to convert a Phylogenetic tree to networkx previously calculated with ...
4 votes
1 answer
65 views

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-...
0 votes
1 answer
106 views

Aligning sequences with multiple genetic codes!

I am doing a project on duplicated genes and I have a major difficulty on how to align sequences that use different genetic codes. I work with fasta files that contain sequences of protein coding ...
0 votes
1 answer
25 views

Defining out-groups in MEGA

I am using the MEGA software for trimming protein sequences and building phylogenetic trees. How can I define out-groups of phylogenetic tree in MEGA? Is there a way to calculate the distances of each ...
1 vote
1 answer
90 views

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 ...
1 vote
0 answers
248 views

getting PDB file of interested sequence

I want a PDB file of DNA sequence I am interested in (10 base pairs) for docking. I will appreciate if any of you can please clarify some of my doubts. Do you think, I can generate PDB file by using ...
2 votes
0 answers
139 views

Fst calculation from VCF files

I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and ...
1 vote
1 answer
40 views

What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?

This question was also asked on reddit Tries are a data structure that can be used to efficiently store and search for strings. Tries created from an ordered sequence of strings differ from the ...
1 vote
1 answer
30 views

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 ...
4 votes
3 answers
578 views

mrbayes, Sumt ; Error when setting parameter "Filename" (1)

question 1 I wanted to use sumt command after completion of mcmc run. Whenever I use, sumt Filename=infile.nex, it gives me the error: ...
3 votes
2 answers
78 views

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 ...
2 votes
1 answer
150 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?
1 vote
1 answer
160 views

Genomics: Downloading genomic data from the NCBI Genbank database

I'm taking a genomics course at school, and we have a final project due in a few weeks. Now, I can write bash scripts to sort and analyze the data, etc. However, I'm not quite sure how to actually ...
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 ...
5 votes
1 answer
701 views

MrBayes runs as single-core, but hangs when multi-core

I compiled MrBayes v3.2.7 from github, with the configuration options ./configure --without-beagle --enable-mpi. The program is called mb. I tried one of the ...
4 votes
2 answers
161 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 ...
3 votes
1 answer
53 views

How can I export a pruned phylogenetic tree in nexus format in R?

I have a phylogenetic tree with a lot of different populations and I wanted to removes most of them and apply new names to the labels. I wrote this code: ...
1 vote
1 answer
93 views

Is 16S sequencing cheaper than whole-genome sequencing for taxonomic assignment?

This is adapted from a question posted on reddit In my work, I occasionally get asked about metagenomic sequencing, which (after further questioning) I discover means that the person wants to work out ...
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 ...
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 ...
2 votes
3 answers
130 views

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

I have multiple lists on python: ...
2 votes
1 answer
58 views

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 - ...
6 votes
5 answers
6k 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 ...
2 votes
1 answer
589 views

Python scripting with ete3 to query NCBI's Taxonomy: "sqlite3 Warning (can only execute one statement at a time)"

I am using this script: ...
2 votes
0 answers
26 views

How come bigWigSummary shows coverage greater than 1 for some region of the genome?

I am running this command, using the UCSC utilities: bigWigSummary -type=coverage ./galGal6.phastCons77way.bw chr4 25526708 25528708 1 to get phastCons77way ...
1 vote
1 answer
63 views

Using average of sequence similarities when delimiting genera - how to deal with outliers?

Sometimes I am trying to see where a (bacterial) genus ends and where another one begins based on 16S rRNA phylogenies. Of course, the length and support of the branch matter a lot, but this question ...

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