Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?
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 regular Tries in the following way:
If there ...
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Problem with setting fixed topology for MrBayes
I need to use partitioned DNA input (concatenated multiple genes) and fixed topology (species tree from ASTRAL) to get branch lengths in MrBayes. I have input NEXUS like:
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How to install DnaSP on a Mac
I need to install DnaSp, a nice GUI originally written for Windows for the population genetics of nucleotide sequence data.
However, its not working on my mac. I'm using wine to install it using these ...
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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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How can extract the list of genes name from the raw data in GEO?
The format of the raw data that upload in GEO is different, like TXT, CEL or other form. How can I extract the list of genes name from these formats? And then how can I normalize them with R?
I would ...
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Build tree to calculate beta diversity
I am trying to calculate beta diversity* using the UniFrac distance on my data, each sample having OTUs values.
To calculate it, I saw it required building a tree with percentages that represented the ...
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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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Is there a way to calculate the number of parsimony informative characters in a morphological dataset in R?
I have a dataset of binary morphological characters and would like to know how many of them are parsimony informative. Is there a way to calculate this with an R package?
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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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Genomics: Downloading genomic data from the NCBI Genbank database
I'm taking a genomics course at school, and we have a final project due in a few weeks.
Now, I can write bash scripts to sort and analyze the data, etc. However, I'm not quite sure how to actually ...
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How to promote assemblies into genomes in NCBI?
Note: I've never submitted an assembly/genome to NCBI, so excuse if my perspective is flawed.
I'm working with Drosophila subobscura. (spring fruit fly)
I see here https://www.ncbi.nlm.nih.gov/data-...
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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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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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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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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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How can I export a pruned phylogenetic tree in nexus format in R?
I have a phylogenetic tree with a lot of different populations and I wanted to removes most of them and apply new names to the labels. I wrote this code:
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UPGMA computation
The unweighted pair group method with arithmetic mean (UPGMA) is a hierarchical clustering method, for example used in phylogeny. In a phylogenetic tree it would result in a global molecular clock ...
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Selection analysis based on each leaves as foreground with FastCodeML
I am using positive selection analysis for each leaves in a phylogenetic tree.
In the routine calculation via codeml, I will be running model zero for all leaves ...
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Is 16S sequencing cheaper than whole-genome sequencing for taxonomic assignment?
This is adapted from a question posted on reddit
In my work, I occasionally get asked about metagenomic sequencing, which (after further questioning) I discover means that the person wants to work out ...
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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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Parsimony-distance neighborhoods in tree space
I have the following question about the paper A parsimony-based metric for phylogenetic trees by V. Moulton and T. Wu.
In this paper, the authors define a "parsimony-distance" between ...
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How to merge multiple list into a single dataframe replacing common values with 1 -python
I have multiple lists on python:
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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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How to create Phylogenetic Trees from fasta files in Python or R?
I have around a hundred Fasta files (and will collect several thousand) with DNA sequences and +50x coverage. What is a recommended method to construct a phylogenetic tree? Solutions in Python or R ...
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Python scripting with ete3 to query NCBI's Taxonomy: "sqlite3 Warning (can only execute one statement at a time)"
I am using this script:
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Single or partitioned model for supermatrix tree inference?
I am dealing with several genes in my dataset. For each of the genes, I have built gene tree, with their best estimated model. I am intended to look into the effect of the tree from concatenated ...
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How come bigWigSummary shows coverage greater than 1 for some region of the genome?
I am running this command, using the UCSC utilities:
bigWigSummary -type=coverage ./galGal6.phastCons77way.bw chr4 25526708 25528708 1
to get phastCons77way ...
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Using average of sequence similarities when delimiting genera - how to deal with outliers?
Sometimes I am trying to see where a (bacterial) genus ends and where another one begins based on 16S rRNA phylogenies. Of course, the length and support of the branch matter a lot, but this question ...
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Scale on the y-axis in a tree rotated with 'layout_dendrogram()' using ggtree
I'm editing a time-scaled tree using ggtree. The dates are correctly adjusted when I apply the 'mrsd' command and 'theme_tree2()', but when I try to rotate the tree with 'layout_dendrogram()', the ...
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Genetic relationships between Cyanobacteria: terrestrial vs aquatic
I believe one of the site members is an expert in Cyanobacteria hence the question.
I'm looking for a comprehensive 'phylogenetic tree' of the phylum Cyanobacteria and want to identify all the ...
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Select synonymous sites from a multiple sequence alignment
Could someone kindly recommend a tool or R package that can identify synonymous sites in a multiple sequence alignment?
I wish to select those taxa for tree reconstruction and other downstream ...
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How do you search for new enzymes that are more stable for handling, immobilization?
Noob here. I get that I should deduce what characteristics the ideal new enzyme should meet, and then use tools such as PDB and blast to compare to the old enzymes, and use other tools such as pymol, ...
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ETE4 manual or improved code description
ETE3 * (Environment for Tree Exploration) is a major package and in particular Python package to navigate phylogenetic trees. It is the premier coding library/package for tree manipulation.
ETE4.0.0 ...
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Pairwise alignment using CIGAR String
I want to perform pairwise alignment and get the resulting CIGAR string (Concise Idiosyncratic Gapped Alignment Report). A fuller description being here
The channel can emit insertions, deletions and ...
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Understanding the fasta file format and using edit distance for alignment
I'm a computer scientist teaching algorithms development in the Fall. One of the algorithms we teach is called Edit Distance, and our folklore is that it is used to compare RNA sequences (is this ...
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Practical use of RNA structure
I have spent some time studying RNA structures. While there is a range of interesting phenomena and functions that certainly deserve understanding from the scientific point of view, I have never ...
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DNA, molecular descriptors
Are there any programs (preferably command line tools) for calculating molecular descriptors of DNA? I am looking for something like Chemopy or RDKit but specifically for DNA.
Thanks in advance!
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Should I compensate for two clusters of samples in microarray by hierarchical clustering and MDS?
I seem to have two groups of samples based on hierarchical clustering as well as MDS plot analysis using the sample label from the tree cut of the hierarchial clustering. I am analyzing microarray ...
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Is there any book or reference that explains evolutionary dynamics and fixation probability?
I am a master's student in computational and mathematical biology, with a bachelor's degree in pure mathematics.
I am really struggling with my computational biology course, we are supposed to study ...
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Phylogeny building in R from FASTA files:
Im working on building a phylogeny from scratch with downloaded FASTA sequences from GeneBank. I think Im doing alright up until the multi sequence alignment in the ...
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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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Removing particular line along with Fasta header in fasta file
I have a fasta file of 3'UTR sequences of the genes. Some of the gene do not have a 3'UTR sequence and reported with sequence unavailable but there is FASTA header.
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Problem with classification model of genomic data: every machine learing model predicts wrongly almost always the same subset of dataset
First of all, I'd like to apologize for any spelling or grammar mistakes.
I'm having a problem using R for a classification problem. My dataset contains ~300.000 genomic data, and the features are ...
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Is there a graphical/interactive 16S rRNA clustering method?
I've been doing phylogenetics with large (hundreds) 16S rRNA sequences lately.
Usually I'm focusing on one order, and using a combination of trees and sequence similarity to assess stuff like 'is this ...
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Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average
I did sequence alignment of a large peptide multi-fasta (n= 4991 sequences). The peptide alignment has sequences with the same length and pal2nal went through just fine... except some of the codon ...
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Fixing FASTA file for Local BLAST Database
I recently prefetched 157 SRA files from an NCBI BioProject using the SRAtoolkit. I then used the toolkit to download those files in FASTA format.
Each individual FASTA file looks something like this:
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How can I run the fdnadist command from the EMBOSS package?
My operating system is Mac OS X.
I would like to compute DNA distances between different sequences. For this, the dnadist package from the Phylip software would be good but hard to automate. EMBOSS ...
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Permutations of 4 amino acid sequence oligopeptide
I have an assignment for a project to build a tetrapeptides library to screen against some target enzymes in silicon.
I am looking for a script to construct about 160000 tetrapeptide from the 20Amino ...
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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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