All Questions
Tagged with phylogenetics fasta
66 questions
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How to remove third codon positions from a charset in iqtree?
I need to build a phylogenetic tree using IQ-TREE, starting from a sequence alignment in CODON format of several invertebrate mitochondrial genes. These are my charsets:
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CommunityBot
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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 ...
- 2,498
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1
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260
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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 ...
CommunityBot
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2
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How to align two FASTAs and extract the aligned part?
I have two fastas and I'd like to align them to extract the aligned part. I've just found examples (Several of them) of alignment of FASTQs using FASTA references, so I'm not sure if what I want ...
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How to know if FASTQ/BAM is from reference genome (FASTA)?
I'm new to bioinformatics. I have a problem in which I have a FASTA reference genome and lots of reads in FASTQ files. Some of them could be contaminants, so I'd like to filter them out and get only ...
- 2,498
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2
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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 ...
M__♦
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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 ...
M__♦
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4
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663
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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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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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M__♦
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How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?
I need to identify the sequence of a gene in the complete genome sequence . I thought it was simple, instead it is not a straightforward task !
My method was the following: I downloaded the FASTA ...
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443
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phangorn fasta file read error
Im trying to read a multifasta sequence file into phangorn I get the following error
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M__♦
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4
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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 ...
- 142
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0
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133
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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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3
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1
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71
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compare fasta sequences in pairs and collect metrics
I have 96 fasta files (A1, A2, A3...) from one plasmid assembly pipeline, and I have another 96 fasta files (B1, B2, B3 ...) from another plasmid assembly pipeline.
I would like to compare pair ...
M__♦
- 13k
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2
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59
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How to obtain desired output?
I am working on a project using the following command within nano:
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M__♦
- 13k
191
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4
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124k
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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...
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M__♦
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147
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How to fix NameError?
I am working on a project and am having issues with the following code that I have written in nano:
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M__♦
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3
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4
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510
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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 ...
- 121
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3
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390
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MiXCR: only create a single export file for all clonotypes
I am using following command from MiXCR to both align, assemble and export my input files:
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3
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Convert a fasta file to Newick format
My problem is (should be) pretty simple.
I have a series of 10 sequences which I wish to convert into a Newick format file - what would be good software to do this? I've tried using Jalview and am ...
M__♦
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3
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2
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125
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How can I resolve "missing name of population" message in PGDSpider?
I want to use Arlequin for AMOVA. I have my FASTA files which I want to convert into .arp files which are recognizable by arlequin. When I try to convert it using Population Genetics Data (format) ...
M__♦
- 13k
3
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1
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108
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Downloading genes from NCBI in fasta format
I'm pretty new in bioinformatics.
I need to download FASTA sequences of several genes. The list of genes I have assembled consists of 140 genes, so I'd rather do this through via code than download ...
- 4,262
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3
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1k
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How can I remove FASTA sequences with an asterisk inside the sequence?
I have several protein sequences with an asterisk in the middle of the sequence, and I'd like to remove those sequences.
In the example below, I have three sequences:
From this example, I would like ...
M__♦
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How to get full headers with tabs as separators with segmasker?
I try to pass a .fasta file with headers where tabs are used as separators as input file to NCBI BLAST+ segmasker:
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M__♦
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Compare and Reorganize Fasta Headers Python
I want to compare the headers from the fasta file to file1, and if there's a match, reorganize the header and put the match first. If there's no match between fasta file and file1, look at file2 and ...
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4
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2k
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multi-sequence alignment of samples with multiple contigs each
I want to perform a multi-sequence alignment on 12 samples that clustered based on cgMLST. Ultimate goal is to find out whether they differ by the presence of a few genes.
I have performed multi-...
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172
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How to chop fasta / bed /peak file genomic segments into smaller fixed or custom genomic intervals
I am trying to split my .bed/.fa file genomic segments into arbitrary smaller overlapping intervals:
Consider a typical line/row in my *.bed file as follows:
chrom. $\ \ \ \ \ $ start $\ \ \ \ \ \ \ \...
- 3,184
2
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2
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447
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Issue with visualising cladogram/phylogenetic tree with multiple sequence alignment data in R?
I would like to visualize tree with multiple sequence alignment.
My din.newick file is shown below,
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- 2,498
2
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2
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445
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Elegant Way to Extract Gene Symbols from FASTA Headers
I've downloaded the RefSeq transcript sequences (FASTA format) for the GRC38 patch 14 build of the human genome and would now like to extract the gene symbols (only) in order from the headers. I'm ...
CommunityBot
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404
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How to know if the DNA sequence has been assembled and why is it important to know how it was assembled?
I have downloaded my FASTA format files, that have the DNA sequences of the coding region of the genes and the DNA sequence of the complete genome, from NCBI. How can I recognize if these sequences ...
- 397
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102
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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 ...
- 15.1k
4
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1
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116
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Counting hexamers in fasta sequence and identify its structure (and interruptions)
I have a lot of fasta files, each one with thousand of reads containing the hexameric motif "CCCTCT". The hexameric motif is highly continuous in most cases but interruptions may occur. I ...
CommunityBot
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1
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47
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Python package or CLI tool outputting mutations of sequence with respect to reference
I'm new to bioinformatics, and I'm looking for a tool that takes two FASTA files, one containing a reference, let's call it A.fasta, the other another sequence, let'...
M__♦
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4
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239
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Programmatic way of accessing the FASTA sequence similarity tool (or similar) in Python
I am looking for a tool that performs a sequence similarity algorithm for proteins. More specifically, I am looking for something that would be usable in Python (or anything else usable in the command ...
- 4,202
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1
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233
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How to get a FASTA format file with the DNA sequences of all annotated genes?
I am analysing Pyrococcus Furiosus DNA sequencing data by considering data published here in NCBI. When I click on "Send to">"Gene Features">"FASTA format" I ...
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94
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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 ...
CommunityBot
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1
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Using Entrez.efetch() to retrive .fasta file from any NCBI database?
I tried to use these python codes to retrieve a .fasta file from gene database, but the output were the parameters of the report
...
- 1,286
3
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2
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425
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Sequence allignment with suffix array?
I'm writing the code from scratch and not using libraries for the actual indexing/search since it's a project for school. Any blackbox advice is fairly useless.
I'm planning on aligning some short ...
- 810
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48
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Combine two alleles to genotype locus?
I have a following fasta (produced by stacks populations):
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- 1,789
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1
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183
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Does anyone know how I can convert DNA code into FASTA for this TTGAAACACTGGATGAATGAAAAGCCCTGCTTTGCAACCCCTCAGC [closed]
TTGAAACACTGGATGAATGAAAAGCCCTGCTTTGCAACCCCTCAGC this is the DNA code Sequence. I have tried converting each into the amino acid and ended up with this LKHWMNEKPCFATPQX but I was told that this isn't ...
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131
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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 ...
CommunityBot
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4
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Tools for comparing/visualizing FASTAs?
I have two FASTAs/assemblies of the same species, but the bases are somewhat different. I would like to explore this.
What tools/methods exist to compare two FASTAs and see the difference in ...
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162
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Get raw genome sequence
I'm currently working on testing some matching algorithms for strings. I would like to do some tests on raw genomic data as I expect different results from random strings given the lower entropy. How ...
- 841
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0
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40
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Please help me with my command!
I am looking for a command to count the total number of unique proteins in a file. For instance I wrote a command to BLAST XYZ proteins as query against the DLY proteins as a database to determine the ...
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1
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47
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Add segregating sites to branches of a tree
I'm trying to figure out how I would plot a tree with number of segregating sites on display on the branches
I'm using acctran from phangorn to plot a parsimony tree (using phydat object from fasta ...
M__♦
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61
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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 ...
CommunityBot
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194
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Weird phylogenetic tree
I am required to create a phylogenetic tree(s) of my genes of interest and am currently blasting (tblastn) my genes of interest from S. mediterranea against model systems before expanding my search.
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M__♦
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34
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4
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9k
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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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M__♦
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3
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301
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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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3
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239
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Effect of mutation in DNA sequence on transcription factor binding sites
How much does a single mutation/alteration of a nucleotide affect the presence of a transcription factor binding site (TFBS)?
I am from computer science background(Obviously).
I want to make a ...
