4
votes
Accepted
Is it possible to do homology inference across species using different kinds of NGS data?
Personally, I would use blastx against a local protein database. This converts query cDNA->amino acids and therefore combines points 1 and 2 without need to ...
M__♦
- 11.9k
4
votes
Accepted
Plot phylogenetic tree from list of edges
The following example uses python to generate the newick string. You can than import that in R for further analysis.
Please keep in mind that you can not use self reference for node4 (9,9,9), so I ...
- 160
4
votes
4
votes
Correlation heatmap of RNA-seq clusters all samples together leading to very low no. of DEGs
This answer has two stages,
Diagnostics, what analytically has gone wrong?
Where to go from here.
I am pretty confident about point 1. I've been in comparable situations and I know trees. Stage 2, ...
M__♦
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3
votes
Accepted
compare fasta sequences in pairs and collect metrics
It's easy; just use output format 6, this gives you a nice table that's easy to parse:
...
M__♦
- 11.9k
3
votes
Read Clustal file in Python
pyMSAviz may help with this problem.
pyMSAviz is a Python tool with a convenient CLI/API implementation for visualizing MSA files.
For example, you can output MSA figure in PDF format with the ...
- 31
3
votes
How can I add a ";" at the end of each fasta header line in a file?
seqkit replace -p "$" -r ";" my.fasta > my.renamed.fasta
Where -p is the pattern to match the end of ...
- 143
3
votes
Accepted
NCBI Blast databases - cannot find some databases
I don't think there is a human_nr or human_nt database for NCBI.
An equivalent database is accessible via the standard nr/nt database and simply restrict the ...
M__♦
- 11.9k
3
votes
Accepted
How to get a GISAID account? I registered months ago, still no reply!
I've got a GISAID account and it's subject to an approval process. It was pretty simple and is awarded quickly. There are definitely no fees needed. I personally didn't see the advantages over NCBI's ...
M__♦
- 11.9k
3
votes
Accepted
How can I export a pruned phylogenetic tree in nexus format in R?
So after digging I found the solution. What worked for me was adding the file = in the write.nexus command. The final line ...
- 339
2
votes
How can I run the fdnadist command from the EMBOSS package?
I found fdnadist in embassy-phylip package https://anaconda.org/bioconda/embassy-phylip
- 21
2
votes
How to programatically download SARS-CoV-2 fasta from NCBI/Genbank via API?
In the efetch.fcgi URL, you can set rettype=fasta to download the nucleotide sequence or ...
- 121
2
votes
Downloading genes from NCBI in fasta format
If I put the species name in quotes, I get expected (by me) output:
...
- 3,804
2
votes
Accepted
How can I resolve "missing name of population" message in PGDSpider?
You could try specifying the population keyword in the record header. From the PGDSpider manual (version 2.1.1.5 (May 2018)), at the bottom of page 67:
Population ...
- 3,059
2
votes
Accepted
Read Clustal file in Python
Ok, figured out a way, not sure its the best one,
nedd to install fpdf2 (pip install fpdf2)
...
- 957
2
votes
Read Clustal file in Python
adding, a second answer because the OP request about
I need to import the file and then highlight some specific word
was making me uneasy. I kept using the Pyfpdf2...
- 957
2
votes
Accepted
Why is COI metabarcoding not used for prokaryotes?
The exact answer to your question is bacteria do not have a mitochondrion, therefore cox1 is not a universal gene combining both Archaebacteria and bacteria. In contrast 16S is universal for these two ...
M__♦
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2
votes
Finding linkage disequilibrium when I have a kinship matrix but not pedigree
I originally thought you were working on humans. I spotted "non model organism", that changes things alot, albeit I guess humans are a non-model organism in a way. The question is what the ...
M__♦
- 11.9k
2
votes
Accepted
Genetic relationships between Cyanobacteria: terrestrial vs aquatic
Ah! Finally, a question I can answer.
There has been some pretty good work about this recently. In particular, I would reccomend this paper by Chen et al. , which groups cyanobacteria into terrestrial ...
- 881
2
votes
Compare substitution matrices
The technique is phylogenetics is called likelihood ratio and for a regular amino acid matrix is 2Δln which is assessed on Chi2 tables where Δln is difference in likelihood between model 1 and model 2....
M__♦
- 11.9k
2
votes
Accepted
How can I convert my tree to the correct nexus format?
Okay ... this will probably work
...
M__♦
- 11.9k
2
votes
Is 16S sequencing cheaper than whole-genome sequencing for taxonomic assignment?
When comparing anything targeted to whole-genome sequencing for the purposes of assembly, the targeted approach will always be cheaper, because the total length that needs to be assembled is shorter. ...
- 13.8k
2
votes
How to create a phylogenetic tree from diverse mitochondrial genomes
It looks like these are random mitochondrial sequences pulled from NCBI, which is probably why the alignments aren't working well.
As a starting point, I recommend you make sure that all the ...
- 13.8k
2
votes
Accepted
How to create a phylogenetic tree from diverse mitochondrial genomes
Your overall approach is cool, given caveats (below) to adapt the method. I can fairly authoritatively say your specific methodological approach will not work regarding its phylogenetic strategy ...
M__♦
- 11.9k
2
votes
What is the best Query to retrieve DNA from NCBI?
There are two main problems I can see in your approach. First, gene names are not standardized across species and the "same" gene (what that means is a whole different discussion) can have ...
- 9,662
1
vote
Accepted
Using ticks on the x axis or a scale bar when visualisizing a phylogram?
Both will work. The convention is the scale-bar and the rationale is below (which is a bit complicated).
By convention:
the right-hand tree where there is a scale-bar and is the traditional diagram ...
M__♦
- 11.9k
1
vote
Accepted
Is there a graphical/interactive 16S rRNA clustering method?
My recommendation is MegaX. It's the closest thing in phylogenetics to an all encompassing GUI.
This has a nice visual alignment editor which highlights conserved, variable and parsimonious sites.
It ...
M__♦
- 11.9k
1
vote
Phylogeny building in R from FASTA files:
The formal question I've been given is what aligner would I use? There is an issue between forming a data pipeline for ape and the latest and greatest. Its trade ...
M__♦
- 11.9k
1
vote
Should I compensate for two clusters of samples in microarray by hierarchical clustering and MDS?
Very interesting, if I understand correctly you are asking whether a straight hierarchical clustering should account for a continuous variable because it is resulting in discrete groups (clusters) ...
M__♦
- 11.9k
1
vote
Is there a way to calculate the number of parsimony informative characters in a morphological dataset in R?
The ape library (Analyses of Phylogenetics and Evolution) using the MPR method (Most Parsimonious Reconstruction).
Information ...
M__♦
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