Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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Transposable elements in phylogenetics
I'm very new to phylogenetics and want to build a cladogram from mammal species using pseudogene fragments. The procedure is as follows:
Find several query sequences from Gallus gallus of the genes ...
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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 ...
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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 ...
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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 ...
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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-...
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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 ...
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Biopython PhyloTree to PyVis Network
We are trying to convert a Phylogenetic tree to networkx previously calculated with
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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 ...
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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:
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Fst calculation from VCF files
I have four vcf files, SNPs_s1.vcf, SNPs_s2.vcf, SNPs_s3.vcf, and ...
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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 ...
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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 ...
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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 ...
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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 ...
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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 ...
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