All Questions
5 questions
2
votes
1
answer
62
views
Compare substitution matrices
I am looking for methods to compare substitution matrices to determine which one is better for a given set of data / type of protein.
Do you know such methods / tools?
e.g. BLOSUM62 vs PHAT for 50k - ...
- 247
1
vote
1
answer
60
views
DNA, molecular descriptors
Are there any programs (preferably command line tools) for calculating molecular descriptors of DNA? I am looking for something like Chemopy or RDKit but specifically for DNA.
Thanks in advance!
- 95
1
vote
1
answer
73
views
Should I expect / use a prokaryote-specific substitution model when building a phylogenetic tree?
I have a couple of prokaryotic genes that I'm trying to build phylogenetic trees from.
I inputted them into IQTree, which, as part of the workflow, runs through multiple substitution models until it ...
- 1,027
1
vote
1
answer
47
views
How to assess if this strategy is good to have some phylogenetic information?
I have several organisms and I want to calculate for each one of these their codon composition implementing a pairwise distance matrix between these codon vectors to build a phylogenetic tree. ...
- 147
4
votes
2
answers
199
views
Motivation behind the neighbor-joining distance matrix recomputation
In each iteration of the neighbour-joining method of phylogenetic trees construction, after joining the nearest neighbours the (additive) distance matrix $D_{m \times m}$ is recomputed as
$$Q_{ij} = (...
- 143