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Questions tagged [phylogeny]

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4
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2answers
74 views

Are phylogenetic tree construction algorithms any different than general clustering algorithms?

I suspect the answer is no. But I don't know enough to be sure that that is the case. Of course phylogenetic tree construction uses biological knowledge, e.g special distance metrics, but does it ...
3
votes
1answer
59 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: ...
1
vote
1answer
64 views

How do I interpret my phylogenetic tree construction from Glucosidases in the Actinobacteria class?

Dear knowledgeable bioinformaticians, I'm currently pursuing an undergraduate degree and as a result I do not have so much knowledge in this topic. I'm having some troubles understanding my ...
3
votes
0answers
28 views
4
votes
1answer
34 views

In calculating the retention index, why do we use the character state with the lowest frequency?

To calculate the retention index for a phylogenetic tree, we use the following formula: $$\frac{\text{maximum number of steps on tree - number of steps on the tree}} {\text{maximum number of steps on ...
2
votes
0answers
33 views

Is there an R package that computes homoplasy excess ratios (HER)?

I want to calculate the homoplasy excess ratio for a phylogenetic tree and a dataset with character states and am wondering if there are any R packages out there that will do this.
3
votes
1answer
92 views

How to assess the quality of assembled .fasta genome files?

I have assembled 3 .fasta files from contigs infastq format of 3 different Homo sapiens. I would like to see if the assembled ...
1
vote
1answer
64 views

A basic question about phylogenetic inference with Bayes-MCMC

I am new to the world world of Bayesian-MCMC inference and have been working my way through various texts. I am having some difficulty understanding how MCMC works. I understand that it is a way of ...
4
votes
2answers
70 views

Do any computational phylogenetic methods enable the specification of ancestral states?

Various phylogenetic algorithms estimate ancestral states of a phylogenetic dataset. Is there a way in either maximum parsimony, distance-based methods, or Bayesian inference to indicate what the ...
0
votes
2answers
47 views

Why does `pratchet()` in `phangorn` not find the most parsimonious trees?

I called pratchet() on a dataset with binary values for the characters and it returned a parsimony value of 35. I then calculated the parsimony value for the ...
3
votes
2answers
152 views

How do I estimate branch length of a maximum parsimony phylogeny in R?

I am trying to estimate a phylogenetic tree in R with ape and phangorn. With pratchet() and optim.parsimony(), I can estimate a ...
3
votes
1answer
61 views

Combine multiple species trees

I have five species trees run using starBeast and Beauti. Here is a link to the paper discussing both, http://journals.plos.org/ploscompbiol/article/file?type=supplementary&id=info:doi/10.1371/...
6
votes
2answers
285 views

How to isolate genes from whole genomes for phylogenetic tree analysis?

I have 446 whole Klebsiella Pneumoniae genomes I want to build a phylogenetic tree from. After reading about constructing phylogenetic trees it seems the only option for large numbers of genomes is to ...
8
votes
3answers
301 views

A tool or webserver for building PSSM matrix

I have some protein sequences and I want to build a position-specific scoring matrix (PSSM) for them and then upload this PSSM to NCBI PSI-BLAST. I used CHAPS program for this pupose but uploading the ...
4
votes
2answers
1k views

How to convert a phylogeny to a dendrogram in R

I want to convert my phylogeny into a dendrogram so I can use it with dendextend in R to produce a tanglegram. I have made some progress but I keep encountering errors, see below: ...
9
votes
4answers
1k views

How do I generate a color-coded tanglegram?

I want to compare two phylogenies and colour the association lines based on some metadata I have. I have been using ape cophyloplot but I have not had any success in getting the lines to colour ...
12
votes
3answers
90 views

What is the best way to account for GC-content shift while constructing nucleotide-based phylogenetic tree?

Let's say I want to construct a phylogenetic tree based on orthologous nucleotide sequences; I do not want to use protein sequences to have a better resolution. These species have different GC-content....
7
votes
1answer
81 views

How does one construct a cladogram of intraspecies relationships?

I have SNP data from several cultivars of rice which I have used to produce alignments, but I don't think that the usual models and algorithms used for generating phylogenetic trees are appropriate, ...