Questions tagged [phylogenetics]
Phylogenetics is the study of evolutionary relationships among biological entities - often species, individuals or genes.
529
questions
1
vote
1
answer
99
views
How can I get data of single cell RNA sequence with raw count?
I am using dataset GSE85241, but I can't find the read counts of the dataset. It only provides with RPKM values.
How can I find the read counts of a dataset?
- 43
1
vote
0
answers
20
views
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 ...
- 11
2
votes
2
answers
62
views
How can I improve or otherwise investigate an unreliable genome tree?
Summary My genome tree doesn't agree with my gene trees and I get the feeling that my genome tree might be wrong, possibly due to long branch attraction, but I don't know how to check/fix it.
...
- 881
1
vote
2
answers
74
views
Generate consensus protein sequence from relatively gappy alignment?
I would like to know what would be the best way to generate a full-length consensus sequence?
I want to obtain a single representative sequence from a relatively gappy multiple sequence alignment of ...
- 2,324
2
votes
1
answer
63
views
ggtree：How to keep leading zero ‘0’ in the tiplabel？
I am using ggtree to draw a phylogenetic tree.
Some taxa IDs have a 0 at the beginning.
However, when I plot the tiplabel the leading zero is automatically dropped. ...
- 81
0
votes
0
answers
158
views
Extract SNPs from multiple sequence alignment
I’m wondering if folks have recommendations for tools/scripts to extract SNP sites from a multiple sequence alignment of consensus bacterial genomes? Specifically, I am interested in a multiple ...
- 111
3
votes
1
answer
78
views
What does this accession NCBI code mean: 6MWN_B?
According to this article, accession codes should consist from a combination of uppercase letters following a combination of digits. If this is a RefSeq, it can have a prefix as a combination of ...
- 435
1
vote
2
answers
123
views
Phylogenetic tree building from proGenomes database for shotgun metagenomics
For some weeks I'm fighting with an issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account phylogenetic distance.
I’m ...
- 41
3
votes
1
answer
52
views
Phylogenetic tree rooting in shotgun metagenomics
But I have some weeks fighting with this issue about phylogenetic tree building to use in a phyloseq object in order to calculate beta-diversity metrics that takes into account tree distance branches ...
- 41
1
vote
1
answer
101
views
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 ...
- 111
2
votes
1
answer
73
views
Biopython reads my tree eternally long
I have a nexus tree (1332 taxa) with a lot of additional data. When I tried to read it through tree = Phylo.read(treepath, "nexus"), my kernel got ...
- 435
3
votes
1
answer
65
views
What is & how to solve File error: my.xml.state (Remote I/O error)?
I caught the next exception during my phylogeographical analysis in BEAST 2 with GEO_SPHERE. What could be the reason? & how to evade this in the future?
...
- 435
4
votes
1
answer
72
views
Tree Building Algorithm that treats gaps as deletions
I'm part of a nanopore sequencing experiment that will sequence several generations of viruses. The intent is to perform directed evolution by putting selective pressure on these viruses and tracking ...
- 51
3
votes
4
answers
897
views
How can I add a ";" at the end of each fasta header line in a file?
I have a large fasta file with RNA sequences. I need to add a ; at the end of each header line (lines beginning with >) in ...
0
votes
0
answers
51
views
What is the best tools to find all the somatic mutations?
I am a beginner in this field. I would like to know which is the best way to get all the mutations from a certain sample. At this point, I am considering using GATK (here) and Maftools (here). I don't ...
- 135
4
votes
2
answers
209
views
What can be the reason of getting negative branches lengths after BEAST analysis?
BEAST2 is currently being used for tree reconstruction prior phylogeographic analysis. The sample size and loci are described below.
I thought that BEAST/BEAST2 does not allow negative lengths of ...
- 435
3
votes
1
answer
102
views
Missing ',' in line when Biopython reads a nexus tree
I want to edit a tree that I got from BEAST2 treeannotator in nexus-format.
Usually I use the module Phylo from Biopython for such work but ...
- 435
2
votes
1
answer
107
views
Is it possible to reconstruct an MSA with PSSM?
I am thinking of reconstructing an multiple sequence alignment (MSA) of protein sequences from a position-Specific Scoring Matrices (PSSM).
Is it possible? I suppose co-evolution information is lost ...
- 289
0
votes
1
answer
298
views
BEAGLE do not see and/or not use OpenCL
I am conducting phylogeny analyses using BEAST 2 as software tool. It is said that it can be accelerated by BEAGLE-library. I have a personal laptop with Windows & a cluster with CentOS.
I ...
- 435
3
votes
1
answer
357
views
What is the meaning of "Filtering allele frequency" in the gnomAD database?
Recent gnomAD versions include a "filtering allele frequency" which tells you when a variant can be safely adjudged not to be disease-causing. Unfortunately, I'm having trouble making sense ...
- 31
1
vote
1
answer
92
views
Convert Arlequin ("DNA" markers) to Genepop (PGDspider or otherwise)
I have Arlequin output files (*.arp) from fastSimcoal2 that I'm trying to convert to genepop files (to read into adegenet). The Arlequin files are using the "DNA" marker (50 bp long), and ...
- 91
-1
votes
2
answers
48
views
How to use GEO_SPHERE?
I have some problems with geosphere package which extends/applies the Beast Bayesian MCMC package for calculating phylogenetic trees. Please, could anyone give any hints about at least one of them?
...
- 435
3
votes
4
answers
367
views
How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?
I would like to download a number of SARS-CoV-2 fastas from NCBI/Genbank using a web endpoint. I looked on their website but it's confusing.
I have the accession numbers, but can't figure out how to ...
- 389
2
votes
1
answer
95
views
Where to get BED files for regions that contain binding site motifs for specific transcription factors?
Quick question, is there a place where one can download BED files for the binding motifs of certain transcription factors. In my case, I'm looking for a BED file for the genomic regions (enhancers) ...
- 29
2
votes
1
answer
69
views
Questions about microbial 16s rRNA phylogenetic, ANI Taxonomy, and GGDC
I have a few questions about these three methods.
We commonly use 16s rRNA to identify species and construct a phylogenetic tree. If there's a new isolate from a new and undiscovered ecosystem, ...
- 51
4
votes
1
answer
151
views
LD Score Regression Derivation hard to follow
I am trying to understand the derivations from Sullivan et al. (2015) in the Supplementary Material. There, it is mentioned in the first page that the least squares estimate of the j-th SNP effect, ...
3
votes
2
answers
778
views
Hirschberg's Alignment Algorithm Implementation. Works on the wiki example but not on large sequences of dissimilar size
I implemented Hirschberg's algorithm in python and used the wiki example to verify correct implementation given the scoring parameters and sequences:
...
- 31
4
votes
1
answer
85
views
Co-occurrence networks in Metagenomics studies
I have recently acquired some 16S metagenomics data, and was wondering if anyone can speak of the potential limitations, challenges as well as advantages to conducting a network-based study on ...
- 836
2
votes
1
answer
35
views
Protein-coding gene evolution age and species divergence time: are they correlated?
Is it possible to infer protein-coding gene evolution age by species divergence time?
For example, species A diverged 300 million years (MYA) ago from its common ancestor with species C, whilst ...
- 289
0
votes
1
answer
90
views
How to solve correlation problems between different samples in scRNA-seq?
I am trying to align and merge different samples from NCBI.
I end up having correlation problem with these sample. The picture below shows an heatmap of the R² by doing a linear regression between 2 ...
1
vote
2
answers
123
views
Bio.codonalign.codonseq module (cal_dn_ds) for SARS-COV-2
I have calculated the dN,dS ratio for a SARS-COV-2 data set ('NC_045512.2' (Wuhan strain) and 'LC666924.1'), and results in a zero value (for most of the genes).
Is it possible and what is the ...
- 11
2
votes
1
answer
204
views
No bootstrap value on single-copy gene tree created by OrthoFinder
I'm running analysis with OrthoFinder and it produces a single-copy gene tree. When I visualize the tree with iTOL, there's no bootstrap value on the branches or nodes. There's a published paper in ...
- 51
3
votes
2
answers
131
views
How to get the number of complete phage genomes available on ncbi?
I am looking to establish the total number of complete phage genomes available on NCBI.
I am not looking for any specific type, but want to understand the total diversity available.
How can I perform ...
2
votes
2
answers
47
views
Is there a publication database or search engine offering geneID or UniProtID correlation?
Do we have a publication database or search engine that offers geneID or UniProtID correlation?
For example, I search "IPS cells" -> I want to know what genes or proteins are under active ...
- 289
1
vote
2
answers
45
views
Mapping NCBI taxID to divergence time?
I want to map NCBI taxID, specifically a pair of Genbank sequences, to the divergence time estimate of their common ancestor. For example, using a coalescence theory approach predominantly used in ...
- 289
2
votes
1
answer
27
views
Independent Subset of Rectangles Problem for Nonoverlapping local alignments
I'd like to implement a graph-based algorithm for DNA comparison, more especially by solving a problem that can be formulated as a Maximum Weighted Independent Set problem.
I have found the article in ...
- 121
1
vote
2
answers
419
views
What is the most appropriate way to find the most recent common ancestor between two distantly related species
I want to specifically find the common ancestor between a lobster and a humans. I suspect it was an aquatic worm of some description. But I want to know about the nervous system of this common ...
1
vote
2
answers
48
views
Remove variable sequence component within a tree text file
I have a gene tree file of 436 orthologue genes from 6 species. I want to remove unwanted extensions as it looks massy after visualization. My file looks like:
(TRINITY_Clupea_DN5452_c0_g1_i1.p1:0....
3
votes
3
answers
243
views
Correspondence of SARS-CoV-2 annotations (Nextstrain clades - Pango lineages)
Is there any annotation file providing correspondence between Nextclade and Pangolin variant nomenclature/annotations, to annotate some SARS-CoV-2 genomes from Gisaid with both these?
For the moment I ...
- 2,676
2
votes
1
answer
64
views
At what point is a gene different between species that we call it a different gene?
I am new to genetics and I know humans share many genes with mice for instance but that there are slight differences in conserved nucleotide sequences. Is there a community consensus around at what ...
- 376
0
votes
0
answers
19
views
Generating intercalation site in DNA for custom sequence
Thank you for your help.
Can anybody please tell me how I can generate an intercalation site in DNA at the base pairs I am interested on. I appreciate if you can please guide me to any tutorials or ...
0
votes
1
answer
122
views
Help me in understanding the PDB file
Can anybody please explain the below line to me.
"We took the structure and coordinates of nogalamycin
from the X-ray structure determined in PDB code = 1D17"
What do I need to download from ...
1
vote
0
answers
33
views
What exactly is a reasonable evolutionary criterion? [closed]
I got a rejection of publication which the reviewers mainly point out as not following a reasonable evolutionary criterion for choice of species used for phylogeny creation. In our dataset, a list of ...
- 11
0
votes
0
answers
14
views
xtract from eutilities not exctracting the information I need
I'm running the following command which uses the NCBI e-utilities:
esearch -db bioproject -query "PRJNA198476 [PRJA]" | esummary
This returns:
...
2
votes
1
answer
81
views
Simulation of DNA sequences through substitution rates
I'm looking for a little bit of guidance.
My question is regarding the simulation of DNA sequences with a fix substitution rate.
The majority of the programs for simulating sequences use Continuous ...
- 23
1
vote
1
answer
64
views
Given SNP-Chip data for a population, what tool should I use to reconstruct haplotypes?
I think Eagle or haploSep will do the job of reconstructing haplotype data, but I'm not sure what the 'standard' or best practice tool to use is.
I have a VCF/PLINK format file of ~8,000 individuals ...
- 470
1
vote
2
answers
75
views
Getting translation table of organisms through Entrez direct (or other CLIs)
I have a long list of NCBI taxonomic ids for organisms and I want to write a script to get their corresponding translation tables. Is there a way to do this through Entrez?
(packages in R, Python etc. ...
- 11
1
vote
1
answer
72
views
building complex drug-dna for AMBER software
I will appreciate if you can please clarify some of my doubts about drug-DNA complex.
I want to study the drug-DNA simulation using AMBER. I did go through all the tutorials video on youtube but ...
0
votes
1
answer
40
views
What to use to determine SNPs in a population? How to find significant SNP variation between generations?
I have a population in the hundreds and did an Illumina pool-seq (ended up with ~100bp reads for the whole population).
I have the reference genome for the species and now need to align all the ...
- 249
1
vote
2
answers
249
views
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 ...
- 11