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Questions tagged [phylogeny]

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2answers
66 views

How to define an outgroup to build a robust amino acid tree

I am trying to build a robust amino acid phylogeny with adequate robustness support (see previous post: How to make a robust amino acid phylogeny with adequate robustness support). This is a brief ...
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1answer
39 views

Weird phylogenetic tree

I am new to research. As part of my MRes, I am required to create a phylogenetic tree(s) of my genes of interest. I am currently blasting (tblastn) my genes of interest from S. mediterranea against ...
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1answer
68 views

How to make a robust amino acid phylogeny with adequate robustness support

This is the second part of this thread: Duplicated genes and genome fragmentation As @Michael G. suggested, I did a pseudo-annotation of sequences 5-2 and 5-3 (i.e., I joined both sequences into one)...
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5answers
88 views

Duplicated genes and genome fragmentation [closed]

This is a follow up question to this post: How can I find out if my gene of interest is duplicated? Briefly, to identify homologous genes, I performed tBLASTn analyses against my genome of interest ...
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2answers
135 views

How can I find out if my gene of interest is duplicated?

To identify homologous genes, I performed tBLASTn analyses against my genome of interest resulting in sequences of a closely related species. Using this method, I found two (and in some cases up to ...
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2answers
32 views

Inferring a phylogenetic tree from BLASTn

I am trying to infer a phylogenetic tree from a Blastn output and from what I have understood, what I should do is 1) extract the alignments and re-align them using Muscle, then 2) feed the .aln file ...
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2answers
89 views

How to find common sequences among 6 multi-fasta files

I have 6 multi-fasta files, every of them contains ca 1500 sequences like that: ...
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1answer
55 views

Are there any resources for calculating / representing evolutionary relationships within gene clusters?

I am working with a gene cluster found in several species. The genes involved are pretty much the same, with the odd insertion, but they can be often found in different orientations. So, I can't just ...
2
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1answer
38 views

Visually summarizing phylogenetic networks

After having worked with Bayesian phylogenetic tree inference for some time, I am now trying out a method to infer network phylogenies. To get an idea of what it infers, I'd like to find a way of ...
2
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1answer
41 views

For phylogenetic tree construction from core-genome which one is preferable: amino-acid based MSA or nucleotide based MSA?

The genomes are from same species. Is it true that, in phylogenetic tree constructed from amino-acid based MSA (multiple sequence alignment) some information are lost, so for phylogenetic ...
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2answers
106 views

Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?

I would like to visualize tree with multiple sequence alignment. My din.newick file is shown below, ...
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1answer
139 views

What do negative dN or dS mean in cal_dn_ds in Biopython?

I'm noobie in bioinformatics. I use cal_dn_ds from Bio.codonalign.codonseq with method 'NG86'. Sometimes I get dS=-1. What does ...
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3answers
207 views

What is the best argument for maximum parsimony method in phylogenetic tree construction?

Beside it (maximum parsimony) being compuationally cheap what other good arguments are there for it? Is there any model behind this principle ? Why would one expect this principle to provide right ...
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2answers
96 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 ...
4
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1answer
160 views

Help interpreting my phylogenetic tree construction of bacterial species in same genus

I constructed a phylogenetic tree using mole blast, and it created a neighbor joining tree, so I used the alignment of those sequences with mine (1-43) in mega with TN93+G+I model but I don't ...
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1answer
130 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: ...
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1answer
100 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 ...
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0answers
34 views

How are the values of prop.part() and prop.clades() calculated?

Consider the following dataset: ...
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1answer
83 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 ...
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0answers
39 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.
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1answer
117 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
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1answer
68 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
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1answer
108 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 ...
4
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2answers
81 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 ...
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2answers
50 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 ...
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2answers
231 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 ...
2
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1answer
281 views

Program to make a haplotype network for a specific gene

Currently my lab manually uses pop art to make the network after using PHASE to id an individual's alleles. Example: I just feel like there's got to be a better, more time effective way to do this.
3
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1answer
73 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/...
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2answers
344 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 ...
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3answers
379 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 ...
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2answers
2k 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: ...
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4answers
2k 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 ...
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3answers
104 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....
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3answers
102 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, ...