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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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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 ...
Peter TSAI's user avatar
2 votes
1 answer
27 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 ...
Mirk's user avatar
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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-...
Mirko'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
  • 143
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1 answer
19 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 ...
user18868's user avatar
1 vote
1 answer
107 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
2 votes
0 answers
90 views

Fst calculation from VCF files

I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and ...
hina's user avatar
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1 answer
102 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 ...
George X.'s user avatar
1 vote
1 answer
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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 ...
GEP's user avatar
  • 111
3 votes
2 answers
73 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 ...
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
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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
135 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
  • 267
3 votes
1 answer
48 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: ...
Nickmofoe's user avatar
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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
74 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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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 ...
gringer's user avatar
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3 votes
1 answer
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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
57 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 - ...
maciejwww's user avatar
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2 votes
0 answers
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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 ...
VeritatemAmo's user avatar
1 vote
1 answer
62 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 ...
Laura'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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0 votes
1 answer
53 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 ...
Gerald Vasquez Aleman's user avatar
1 vote
1 answer
43 views

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
234 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
  • 237
1 vote
1 answer
54 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
67 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
129 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
  • 111
2 votes
0 answers
124 views

Phylogenetic tree from a large FASTA file

I want to create a phylogenetic tree using a 3.8MB FASTA file with ambiguous code. How can I perform multiple sequence alignment and the construction of phylogenetic tree with these ambiguous codes? ...
user17615's user avatar
1 vote
1 answer
247 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
  • 149
1 vote
1 answer
82 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
130 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
261 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
290 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
36 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
204 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
56 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
47 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
66 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
56 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
3 votes
1 answer
251 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
1 vote
0 answers
56 views

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 ...
M__'s user avatar
  • 12.3k
2 votes
1 answer
131 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
  • 963
2 votes
1 answer
76 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
  • 909
3 votes
1 answer
83 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
101 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

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