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 ...
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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 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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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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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 ...
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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 ...
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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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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 ...
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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 ...
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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 ...
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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 ...
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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 - ...
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