Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
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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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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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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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How to get phylogenetic tree from multiple genes?
I constructed a phylogenetic tree using a gene (example - secA). I had to gather the same gene sequence for all the required species from public database-NCBI and then constructed the tree after ...
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Kraken2 > OTU format > Phyloseq
A collaborator has passed me over Kraken2 outputs *.report and *.kraken, from a metatranscriptomic sequencing experiment conducted on the minION.
I would like to make a tree if the data using a ...
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How are BLAST record scores calculated in biopython
Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is ...
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Can't load files into PopART
I am trying to create haplotype networks in PopART (Population genetics with Reticulated Trees*) which I have successfully done many times in the past.
Two weeks ago the program was working fine for ...
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How are the values of prop.part() and prop.clades() calculated?
Consider the following dataset:
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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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Phylogenetic tree from a large FASTA file
I want to create a phylogenetic tree using a 3.8MB FASTA file with ambiguous code. How can I perform multiple sequence alignment and the construction of phylogenetic tree with these ambiguous codes?
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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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Why does segmasker modify headers?
When parsing NCBI BLAST+ segmasker output, I realized the program modifies almost every header containing these strings: ( or )...
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Is there a DNAWeaver How-to guide?
Recently I've been trying to use DNA Weaver for customized gene assembly design.
Although there is a web version that allows to perform some assembly examples, I've tried to replicate them with python ...
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Calculate interval of flanking introns
I am looking for a easy way to calculate the intervals of flanking introns based on a transcript annotation file. I have chosen a very complicated method:
...
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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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Cannot blast against specific NCBI databases
I am having issues with some prokaryote reference genome databases (exact names : ref_prok_rep_genomes.*), that I downloaded from the NCBI website : https://ftp.ncbi.nlm.nih.gov/blast/db/. Files in ...
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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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How to get bootstrap support of phylogenetic tree?
I have used multiple sequences aligned file of protein data to generate a maximum parsimony tree, then I used the "bootstrap_trees(msa, times, tree_constructor)" ...
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Does anyone have older versions of NT and 16s RNA DB from NCBI?
I am in search of past years' versions of NT and 16s databases from NCBI. I recently contacted NCBI about this and they replied:
Unfortunately, we do not archive past versions of the blast ...
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Reproducing population structure from 1000 Genomes Data
I recently tried to reproduce population structure with 1000 Genomes Project data (Phase 3, 2504 people).
According to supplementary material,
To reduce the dataset, we used VCFtools to only keep ...
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Alignment using secondary and tertiary features of DNA
I m trying to align different sequences of length not greater than 50 bp. Could I incorporate additional information such as stacking energy, entropy, bonds etc as additional criteria in the alignment?...
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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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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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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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How to identify all descendents of a branch on a phylogeny
I'm trying to simulate the evolution of binary traits on phylogenies in R to end up with a dataset of the traits held by each tip. Starting at the root, at every timestep, new traits are added with a ...
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eggNOG API, how's it work?
Background eggNOG uses seed orthologues which correspond to its own internal database, so for example J421_1876 can be placed in its online search engine here. This ...
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segmasker doubles found intervals
During NCBI BLAST+ segmasker output exploration, I found out that for some sequences, the program returns the same interval twice:
...
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Using information criteria weights to create consensus tree
While I am familiar with calculating information criteria for various ml models of a multiple sequence alignment, I am not aware of how to use the derived weights to create a tree that combines ...
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I want to map TFBS on to the sequences from dataset containing 8448 (210 base) sequences. its not giving all the hits I need
I want to map TFBS (transcription factor binding sites) on to the sequences from dataset containing 8448 (210 base) sequences, but it is not giving all the hits I need
...
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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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Calculating the effect of differences between two groups of nucleotide sequences at every position
I'm investigating two different groups of short nucleotide sequences. The behaviour of a certain DNA-binding protein is likely influenced by common differences between these two groups leading high or ...
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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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Downloading exon-wise gene sequence using commandline
I want to download exon-wise gene sequence of around 200 genes from NCBI. Is there anyway to do this from terminal? I have the transcript id for each sequence and I am using efetch command to download ...
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Tool that can sort NCBI taxonomy ids based on phylogeny
I have a set of NCBI txids (of varying ranks) that I want to sort in some way (e.g. a table or a tree, the way it is sorted isn't super important), based on the current NCBI data for phylogenetic ...
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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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How to decide whether to assume 2 Gene Losses or 1 to find minimum cost trees for Gene Duplication/Expression events?
This paper introduces an approach to estimate a convergence from discord between phylogenetic species trees and gene trees, using Gene Duplication and Expression events.
A Gene Duplication (GD) event ...
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How to interpret complete genome sequence in NCBI
I have a very basic and quick question: does the complete sequence of nucleotides of an organism (for example this one that I am considering in my homework of Pyrococcus Fuoriosus) reported in NCBI ...
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Computing Maximum Agreement Subtree of two unrooted phylogenetic trees with PhyloNet?
I am using PhyloNet to compute the MAST of two unrooted binary phylogenetic trees but I am not getting the output that I should. I think the issue might be with the way I am writing the trees in the ...
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How to read E-value annotation on NCBI BLAST?
I am seeking clarification on how to read the E value annotation on NCBI's BLAST results.
What I understand so far:
E -values are the expected value of the number ...
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PCA analysis and nucleotide diversity pi
I have 25 individuals' whole-genome sequence (collected from 5 different locations) and after doing a variant calling analysis, I found 2734 SNP+INDELS marker (SNPs + INDELS = 2734 ). Then I plotted ...
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How to deal with the mismatches between gene names obtained from different sources?
For most of the time, I rely on gene ids to combine different datasets. However, in some instances, I have to combine datasets based on gene names. Then, if I don't know the source of gene names in ...
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Comparison of phylogeny of SARS2 whole genome vs spike genome
I’ve built two phylogeny at minimum evolution in MEGA-X and extracted these as newick files.
My next step is to compare the two phylogeny to look at if the mutations within SARS2 are more prevalent ...
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"How the clustal omega can be reverse engineered, to trace ancestral inversion mutations via the guide tree?"
I apologise for very basic question but I am very new to biology and have very specific knowledge of this field, I am currently working on Bioinformatics in my machine learning project which is why I ...
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How many markers or loci are used in forensic DNA profiling and the effect of the DNA sequencing?
I am reading the Wikipedia page on DNA profiling, specifically STR analysis. It says that DNA profiling relies on matching 20 or so loci. It also gives an account of finding false identification. But ...
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Generating taxonomic hierarchy by species/genus name
I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a ...
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What steps should I follow for DNA analysis, for a classification problem?
I have a bed file which contains DNA sequences information as follow:
**
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mining DNA barcodes from Genebank/BOLD per location
Is there a method to download all the sequences for a particular geographic region (Panama) for 'DNA barcode' sequences (ITS2, rbcL or trnL). Hopefully, the specimen collection location will include ...
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Is there a software that can predict protein-DNA binding?
Is there any software that, given a DNA sequence as input, can predict what protein/ type of protein can bind to the DNA. The sequence of interest is a potential transcriptional regulator, I want to ...
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How to (efficiently) search nuccore to retrieve only annotated sequences?
I wish to efficiently search nuccore to retrieve only annotated sequences.
By "annotated" I mean that the nuccore entry contains annotation information.
An equivalent definition (if I understand ...
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Is there a built-in parser for the textual feature table that Entrez.efetch returns?
Entrez.efetch helpfully gives me the feature table of a nuccore entry.
If I understand correctly, efetch can only return the ...
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