All Questions
Tagged with phylogenetics fasta
66 questions
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113
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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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- 247
1
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2
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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 ...
- 2,364
1
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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 ...
- 121
1
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1
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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 ...
- 1,027
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1
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143
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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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1
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0
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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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- 11
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2
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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 ...
0
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2
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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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1
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2k
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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
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- 15
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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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0
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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 ...
0
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1
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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 ...
- 317
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1
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26
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SRA Toolkit and lebanese data
I am trying to extract data from this:
https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR6245218
I installed SRA Toolkit, downloaded the SRR6245218 file and executed this:
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- 359
0
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1
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50
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Function to find ATP binding sites
I'm currently doing a python project where I need to write code that extracts the ATP binding site from a FASTA file using a regular expression.
I've tried the following code but it does not work. It ...
0
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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 ...
- 15
-1
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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 ...
