Questions tagged [phylogenetics]

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

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Why does the SARS-Cov2 coronavirus genome end in aaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaaa (33 a's)?

The SARS-Cov2 coronavirus's genome was released, and is now available on Genbank. Looking at it... ...
Rebecca J. Stones's user avatar
34 votes
4 answers
9k 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: ...
jameshfisher's user avatar
27 votes
4 answers
6k views

Why sequence the human genome at 30x coverage?

A bit of a historical question on a number, 30 times coverage, that's become so familiar in the field: why do we sequence the human genome at 30x coverage? My question has two parts: Who came up ...
719016's user avatar
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21 votes
8 answers
9k views

What is the fastest way to get the reverse complement of a DNA sequence in python?

I am writing a python script that requires a reverse complement function to be called on DNA strings of length 1 through around length 30. Line profiling programs indicate that my functions spend a ...
conchoecia's user avatar
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21 votes
8 answers
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Since every human has a different DNA (different combinations of C, G, A, T) what does it mean to have the genome done? [closed]

I'm confused about the difference between genome and DNA. Is it correct to say that the same type of bacteria has the same DNA? But my understanding is that it is not correct to say that the same type ...
CCCCoder2's user avatar
  • 319
19 votes
2 answers
645 views

Accuracy of the original human DNA datasets sequenced by Human Genome Project?

The Human Genome Project was the project of 'determining the sequence of nucleotide base pairs that make up human DNA, and of identifying and mapping all of the genes of the human genome'. It was ...
kenorb's user avatar
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19 votes
1 answer
2k views

Is it possible for coronavirus or SARS to be synthetic?

I have heard several conspiracy theories regarding the origin of the new coronavirus, 2019-nCov. For example that the virus and/or SARS were produced in a laboratory or were some variant of Middle ...
Sscheme's user avatar
  • 303
14 votes
2 answers
300 views

Is there a standard k-mer count file format?

I am doing a research project involving calculating k-mer frequencies and I am wondering if there is any standard file format for storing k-mer counts.
Jon Deaton's user avatar
14 votes
1 answer
2k views

Biopython Phylogenetic Tree replace branch tip labels by sequence logos

Having recently constructed a lot of phylogenetic trees with the module TreeConstruction from Phylo package from Biopython, I've been asked to replace the branch tip labels by the corresponding ...
Boris Schnider's user avatar
13 votes
3 answers
7k views

What is a quick way to find the reverse complement in bash

I have a DNA sequence for which I would like to quickly find the reverse complement. Is there a quick way of doing this on the bash command line using only GNU tools?
winni2k's user avatar
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13 votes
3 answers
168 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....
Iakov Davydov's user avatar
12 votes
5 answers
349 views

Improve a reference genome with sequencing data

I have a DNA sample which I know doesn't quite match my reference genome - my culture comes from a subpopulation which has undergone significant mutation since the reference was created. The example I ...
Scott Gigante's user avatar
11 votes
5 answers
21k views

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. ...
MudithMMBc's user avatar
11 votes
1 answer
2k views

What is the best method to estimate a phylogenetic tree from a large dataset of >1000 loci and >100 species

I have a large phylogenomic alignment of >1000 loci (each locus is ~1000bp), and >100 species. I have relatively little missing data (<10%). I want to estimate a maximum-likelihood ...
roblanf's user avatar
  • 952
11 votes
1 answer
370 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 ...
Iakov Davydov's user avatar
10 votes
4 answers
4k 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 ...
AudileF's user avatar
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9 votes
3 answers
2k views

A new paper suggests the Corona Virus has "Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1" - What does this mean?

Quote: We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have ...
SurpriseDog's user avatar
8 votes
4 answers
11k views

What reasons are there to choose Illumina if PacBio provides longer and better reads?

PacBio provides longer read length than Illumina's short-length reads. Longer reads offer better opportunity for genome assembly, structural variant calling. It is not worse than short reads for ...
SmallChess's user avatar
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8 votes
2 answers
2k views

What is 'k' in sequencing?

When a DNA sequence is sequenced, I've only ever dealt with A,T,C,G and N which indicates un-identifiable bases. However, I came across a 'k' recently and I had asked another researcher who gave me an ...
Jonathan's user avatar
  • 341
8 votes
2 answers
483 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 ...
Daniel Harris's user avatar
8 votes
3 answers
147 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, ...
twmccart's user avatar
  • 133
8 votes
3 answers
2k 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 ...
Sara's user avatar
  • 767
7 votes
3 answers
1k views

Importing GFF file with Biopython

Is there a way to import a GFF file for an organism with Biopython in the same way you can for a Genbank file? For example, ...
Alex Summers's user avatar
7 votes
2 answers
666 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 ...
Sidra Younas's user avatar
7 votes
1 answer
401 views

ANY (technical) reason behind submitting sequences to GenBank versus ENA Sequence

The DNA sequence sections of the three INSDC databases (i.e., DDBJ, ENA Sequence and GenBank) are synchronized periodically and strive to keep their stored data as ubiquitously accessible as possible. ...
Michael Gruenstaeudl's user avatar
7 votes
1 answer
86 views

Source for whole genome comparisons at NCBI Genomes

The NCBI Genomes database has these dendrograms for (presumably) whole genome comparisons for certain species, e.g. Pseudonomas aeruginosa or Escherichia coli. How were these comparisons done? ...
Peter Menzel's user avatar
6 votes
5 answers
6k views

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 ...
Soerendip's user avatar
  • 1,295
6 votes
2 answers
451 views

Theoretical limit of human genome compression

How small can a compressed file containing the human genome be? I'm aware that this question cannot actually be answered, since it is asking for the Kolmogorov complexity of the human genome, which is ...
Rexcirus's user avatar
  • 171
6 votes
2 answers
1k views

Are phylogenetic tree construction algorithms any different than general clustering algorithms?

Are phylogenetic tree construction algorithms any different from clustering algorhithms? I suspect the answer is no. Of course phylogenetic tree construction uses biological knowledge, e.g special ...
Ahmed Abdullah's user avatar
6 votes
4 answers
3k views

Convert rs ID of one hg build to rs IDs of another build

I have a list of dbSNP rsIDs for GRCh37 and I want to convert them to the equivalent IDs in GRCh38. This is using the most recent dbSNP build (150 as of the time of this post). Is there any ID mapping ...
Rob John's user avatar
  • 221
6 votes
1 answer
441 views

Biohackers Netflix - DNA to binary and video

I'm not sponsored or anything, just interested in their challenge to decipher their DNA code. They encoded their first episode of "Biohackers" video/binary file to DNA code and said if we ...
xamax 's user avatar
  • 63
6 votes
1 answer
342 views

What is Allelic Imbalance

Can anyone help me explain what allelic imbalance is, hopefully shortly? Surprisingly, we cannot find any introduction online.
Haohan Wang's user avatar
6 votes
1 answer
148 views

Getting all NNI trees of a parsimony tree

I have an aligned protein sequence file which I have been using for reconstructing a parsimonious tree. I am currently using NNITreeSearcher._get_neighbors method from Biopython 1.72 but it's way to ...
Sidra Younas's user avatar
6 votes
1 answer
87 views

State of the art in predicting Translation Initiation Sites

I'm working on a university project of predicting Translation Initiation Sites in human DNA. I searched the net for papers and documentation to get guidelines and inspiration, but I feel uncertain ...
user avatar
6 votes
1 answer
129 views

How to search for high coverage SRA entries

The Question I want to find high coverage SRA entries, e.g., above 100x. I guess the best way is to use https://www.ncbi.nlm.nih.gov/sra with an appropriate search term. I don't mind if the search ...
Oren Milman's user avatar
6 votes
1 answer
219 views

What is the minimum number of individuals per group required for ADMIXTURE analysis?

What is the minimum number of individuals required per group (population/species) for an ADMIXTURE analysis to be appropriate? Is there a way to determine this number mathematically based on the ...
Erin Thompson's user avatar
6 votes
0 answers
98 views

making my own population allele frequency table for input to IADMIX from Gnomad data (population admixture)? [closed]

Hi I'm a first time user of IADMIX. I tested on one known Finnish sample from the 1000Genome project using the softwares provided frequency table hapmap3.8populations.hg19.freqs and the prediction is ...
Sam's user avatar
  • 61
5 votes
6 answers
3k views

How to extract metadata from NCBI's short read archive (SRA) for a few runs?

I wish to extract metadata from a list of runs on NCBI's short read archive. For instance, I'd like to extract the library name ("HS0798") from the following run info: https://trace.ncbi.nlm.nih.gov/...
init_js's user avatar
  • 319
5 votes
1 answer
87 views

Why does the SARS-Cov2 genome has letter t [duplicate]

ATTAAAGGTT TATACCTTCC CAGGTAACAA ACCAACCAAC TTTCGAT... is part of the 5'UTR of genome of an RNA virus SARS-Cov-2. RNA contains letters ...
Pavel Pelan's user avatar
5 votes
3 answers
2k views

Way to get genomic sequences at given coordinates without downloading fasta files of whole chromosomes/genomes first?

So I have a list of start and stop positions along chromosomes in different species, and I'd like to get the corresponding DNA sequence for each set of coordinates. In the past, I've just download the ...
Eric Brenner's user avatar
5 votes
3 answers
4k views

How to translate amino acid sequences to Nucleotide sequences

I want to convert a list of fasta ( protein sequences) in a .text file into corresponding nucleotide sequences. A Google search gives me result of DNA to protein conversion but not vice versa. Also, I ...
user3289492's user avatar
5 votes
2 answers
137 views

Can we describe synthetic biological sequence data as belonging to a "species" or "taxon"?

For the purpose of testing phylogenetics software, we're using synthetic sequence data (i.e., it's computer generated, and there's no actual biological organism with that e.g. DNA sequence). For real-...
Rebecca J. Stones's user avatar
5 votes
2 answers
2k views

What does PCA mean on GWAS

I understand what GWAS is and I'm able to perform certain tests with the p-values, etc. But what I am having a hard time wrapping my head around is what PCA on GWAS means. So let's say I have 100,000 ...
Jonathan's user avatar
  • 341
5 votes
2 answers
152 views

Counting letters in phylip alignment columns with Biopython

I have been using python 3.6 and biopython 1.72 to work with protein data files. I am using a protein sequence file (phylip format), for example: ...
Sidra Younas's user avatar
5 votes
2 answers
274 views

Calculate the percentage of each unique phylogenetic tree in a BEAST output

I have a nexus formatted BEAST output containing 20,000 phylogenetic trees of seven taxa. Is there any way to get the percentage of each unique phylogenetic tree contained in this output? I already ...
jvddorpe's user avatar
  • 191
5 votes
1 answer
895 views

Ancestry of the coronavirus 2019-nCov, WuHan city, China

In one of the answers to another question about the corona virus a link was given to this phylogenetic analysis of the virus. Can somebody assist a non-bio type here? It seems to show that the ...
puppetsock's user avatar
5 votes
2 answers
164 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 ...
Dandelion's user avatar
  • 153
5 votes
2 answers
134 views

How do population genetics people define a population?

How do population genetics people define a population? Do they define it as a layman will do? say Africans, Americans, or so? Or is there a more scientific way of doing so? For example, I think ...
Haohan Wang's user avatar
5 votes
3 answers
1k views

How to automate NCBI genome download

I need to download all the completely assembled cyanobacterial genome's GenBank file(.gbff) from NCBI(RefSeq or INSDC ftp data). For this I think, the steps are: Need to find the completely ...
Arijit Panda's user avatar
5 votes
1 answer
4k views

Why do NEBNext indexing primers have sequence between the p5 oligo and index?

In a previous post I asked Why do NEB adapters have non-complementary sequence? Since then, I realized that there is some other sequence in the p5 indexing primer, as well as in the p7 indexing ...
conchoecia's user avatar
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