Questions tagged [phylogenetics]

Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.

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1answer
89 views

which NCBI tool is optimized to identify a species from a DNA fragment?

“The Iceman” was a man who lived 5300 years ago and whose body was recovered from an Alpine glacier in 1991. Some fungal material was recovered from his clothing and sequenced. Ice man : found as a ...
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1answer
28 views

After KEGG and GO analysis, how to make tables+phylogenetic trees

hope everyone is ok. I used Trinity to do a de novo transcriptome assembly, then blastp/blastx and then used Blast2GO software to do KEGG and GO analysis. So i got some txt files with header : for GO ...
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4answers
138 views

Comparing phylogeny in R

So I want to compare the phylogeny created using two methods for example Maximum likelihood and maximum parsimony.Is there any way to compare the two phylogeny ? I did read about phangorn but not ...
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2answers
102 views

16S species-level taxonomic assignment--what is the current state of the art?

We currently use DADA2 for picking ASVs and the assignTaxonomy funciton for assingment to genera. Google does bring up various recent articles on species-level ...
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1answer
231 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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41 views

Relationship between the instantaneous rate of change of a continuous time Markov model and the rate of a global clock model?

If continuous-time Markov models contain a parameter q that denotes the instantaneous rate of change and a global/strict clock model is the overall rate of evolution, how are these two parameters ...
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1answer
15 views

Phylogenetics software that can represent collapsed nodes as triangles

I am trying to represent a large (100-300+ sequences) phylogenetic tree in a way that gets my point across. I figured that reducing the number of branches (by collapsing clades which include highly ...
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1answer
14 views

phangorn fasta file read error

Im trying to read a multifasta sequence file into phangorn I get the following error ...
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1answer
74 views

a package with randomization/permutation tests for genomic analyses

please would you let me know, is there a package in R/python/C that has implemented randomization/permutation tests for joint genomic analyses (an example of joint genomic analyses -- when jointly ...
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1answer
75 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 ...
4
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1answer
133 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 ...
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1answer
391 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.
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1answer
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How to construct the phylogenetic tree of the “High Recombination” genus streptomyces?

I need to construct the phylogenetic tree of the whole genus of streptomyces. And my goal is to find out how my target strep species distributed in the whole strep genus and obtain the distribution ...
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1answer
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Algorithmic investigation of viral proteins for vaccine design [closed]

I wish to investigate how a virus could be attenuated through targeted mutagenesis by investigating its protein mutations in order to produce an efficacious vaccine. Are there examples where the ...
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8k views

Why does the FASTA sequence for coronavirus look like DNA, not RNA?

I'm looking at a genome sequence for 2019-nCoV on NCBI. The FASTA sequence looks like this: ...
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1answer
195 views

Issues installing Dendropy

I want to perform phylogenetic analysis using Dendropy. I have installed dendropy using command sudo pip install -U dendropy but when I import it in python3.5.1 it ...
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1answer
77 views

Random addition method for phylogenetic tree reconstruction

I have been working on nucleotide and protein data to reconstruct maximum parsimony trees using MEGA software to get parsimony tree, via "random addition" method is used to generate the initial tree(s)...
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1answer
129 views

What is a site in a phylogenetic tree?

When I read about a term related to phylogenetics, for example, $K_a$/$K_s$ ratio, I constantly see the word site, whose meaning isn't explained and it puzzles me. For example substitutions per ...
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1answer
154 views

Test to determine if two genes/exons share the same evolutionary histories?

In classic phylogenetic inference one is usually given various orthologue sequences of a given gene across various species. Those sequences are then multiple aligned and used to construct a ...
4
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1answer
169 views

Problems in creating desired phylogenetic tree with ggtree

I am working on haplotype data and want to make a tree out of haplogroups using ggtree. I have following data in newick format. ...
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202 views

How to create a dendrogram of clusters and reconstruct phylogenetic relationship

I'm working with a Daphnia data set looking at the 16s gene pulled from the BOLD database. So far I did a multiple sequence alignment and attempted to cluster and plot a dendrogram: ...
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2answers
433 views

What is outliers and how to determine outliers in the following phylogenetic tree?

I an confused with the term 'outlier' and 'outgroup' in phylogeny. Could someone please explain with the example phylogenetic tree above which is the correct term? Thank you very much !!!
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1answer
320 views

Does the “.full.aln” file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?

I have a number of sequences and a reference genome. I used snippy to align each individual sequence with the reference genome. I then used ...
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1answer
68 views

How do I interpret the function O(f^-2 log n) in Shekhar et al. (2017)?

The results of Shekhar et al. (2017) "indicate that ASTRAL requires $\mathcal{O}(f^{-2} \log{n})$ gene trees to reconstruct the species tree correctly with ...
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1answer
215 views

MrBayes runs as single-core, but hangs when multi-core

I compiled MrBayes v3.2.7 from github, with the configuration options ./configure --without-beagle --enable-mpi. The program is called mb. I tried one of the ...
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2answers
173 views

Truncating branch length values of Phylogenetic tree with biopython

I have been using biopython 1.72 to display my phylogenetic tree files. Using the function 'Phylo.draw(pars_tree, branch_labels=lambda c: c.branch_length)' to ...
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2answers
88 views

Perfect Phylogeny vs Maximum parsimony

I am searching various sources about phylogenetics. I saw some materials about perfect phylogeny and also phylogenies acquired from maximum parsimony constraint. They seem very similar to me. Are they ...
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0answers
51 views

Common Mouse and human DEG analysis

I have DEGs from human and mouse (equivalent of a human disease model), and aim to generate a logCPM correlation plot between the overlapping mouse and human gene (275 genes). Prior to joining, mouse ...
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0answers
70 views

How snippy makes MSA-like aligned fasta output from multiple samples?

From the log file it seems snippy doesn't do assembly. It only does mapping: fastq --> SAM --> BAM --> VCF --> consensus_seq/snps But if multiple ...
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3answers
1k views

How to create Phylogenetic Trees from fasta files in Python or R?

I have around hundred fasta files with DNA sequences with good coverage, what is a recommended method to construct a phylogenetic tree? Solutions in Python or R are sought. I found ...
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2answers
137 views

How to plot character state changes from a presence-absence matrix on to a phylogeny

I wish to assign character state changes from a presence-absence matrix to a phylogeny. Thus I want to identify the most parsimonious hypothesis for which node and branch a given "mutation" or "change"...
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1answer
43 views

Confusion related to effective population size

I am making a demographic model for African American population in which I say 80% of ancestry comes from African population and 20% comes from European population. I am using the time/population time ...
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1answer
31 views

Calculating Unifrac Distance and missing data

I am trying to calculate unifrac distance for my OTU table, which has about 3000 taxa, and 300 samples. My phylogenetic tree only considers the most important 500 taxa. My questions are: Do I ignore ...
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2answers
149 views

PDB file downloading: pymol automation vs. manual

I automated a PDB download using a Pymol script (below) ...
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2answers
55 views

Protein model quality assessment

How do I perform protein model quality assessment? I will obtain predicted structures from DMPfold, I-Tasser, and Rosetta, what should be the next approach to select a structure from among this set ...
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0answers
52 views

Calculating the trimming parameter when constructing an additive phylogeny

How do you calculate the trimming parameter when constructing an additive phylogeny? I think it has a relationship with the the length of the shortest hanging edge but I can not figure out how this ...
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1answer
340 views

State of the art mutation simulation software

There are many features affecting mutation probabilities, e.g. CpG mutations are 10-fold more likely than other types of mutations. Is there a model (preferably with software) which can take two ...
2
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1answer
47 views

How to extract hypervariable region of mitochondrial dna from its fasta file?

Recently I've done some analysis on human mitochondrial DNA and now I want to run the same analysis on only hypervariable regions of mitochondrial DNA to see whether the changes that I have observed ...
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1answer
57 views

Interpreting quantitive outputs from maximum likelihood phylogenetic trees

I ran a calculation in RAxML to determine the majority consensus phylogeny of a maximum likelihood bootstrap (How to show bootstrap values on a phylogenetic tree constructed with RAxML), and I got ...
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0answers
33 views

Algorithmic Information Measurement of Human Genome Databases?

What is the highest data compression ratio achieved on a population of genomes measured to include the compressing algorithm itself? The size of the compressed database approximates its algorithmic ...
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1answer
29 views

What software can I use to develop a population haplotype network?

I looking for software to conduct a haplotype network using cytochrome oxidase (CO1) mitochondrial sequence data to study population structure in Anopheles mosquitoes.
3
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1answer
74 views

How to interpret UniProt allele patterns?

In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the comments POLYMORPHISM there ...
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2answers
52 views

efetch nucleotide -> protein ids

I'm downloading translated viral genomes initially via Blast - which had shortcomings - and now by efetch. What I want to do is obtain a complete list of all ...
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1answer
54 views

How to allow “half windows” in biopython?

I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window ...
4
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1answer
236 views

How to find which scales are available in SeqUtil of Biopython?

I am trying to analyse the hydrophobicity of a sequence using BioPython's "SeqUtil". ...
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1answer
36 views

Why do we scale the rate matrix of a substitution model to make the average rate of substitution equal 1?

The matrix of transition probabilities for a substitution model Q over time t is found as follows: $e^{Qt}$. Since Q and t only show up as a product, we cannot distinguish time and rate of change. So ...
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2answers
630 views

How to show bootstrap values on a phylogenetic tree constructed with RAxML

I apologize for this very basic question. With @Michael G.'s help, I have been learning how to use RAxML to build a phylogenetic tree (How to define an outgroup to build a robust amino acid tree) and ...
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1answer
130 views

Crossover question from Coding Theory

I have a model that, for a given bit of code will produce a binary string. An example is given 01010101, it might produce {1,11}, and given 01010000, it may produce {2, 11}. I have a lot of these ...
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0answers
64 views

Help with identifying disease modules

I've made an application that at this point ranks all combinations of drug pairs relevant to a biological network/graph in the order of how disruptive the outcome of deleting the targets of a given ...
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2answers
43 views

Download sequences of isoforms

I want to collect all isoforms of all genes (Fasta/Fastq file of nucleotide and protein sequences) Arabidopsis Col-0. I am wondering if there is a straightforward way to download the file from any ...