Phylostars: Sample Questions and Answers
examples from other places
- from evoldir's archive
- how to concatenate MSAs a synopsis of answers. Needs links and references. Could be worked up into a brief tutorial.
- from Bodega Bay phylogenetics workshop, some tutorials. Some of these are heavyweight (e.g., 15 pages of instruction about BEAST), but others are more like a brief tutorial (garli, gamma dist).
examples from biostars
These are examples with lots of votes or views. Some of them are framed in a good way for a tutorial, and some of these have answers that could provide a good starting point.
Note the HowTo section: http://www.biostars.org/show/howto/
and also with the tutorial tag: http://www.biostars.org/show/tag/tutorial/
Istvan says that sorting by views or votes is a good way to find the highly appreciated ones.
Best ranked on BioStars
most these have 15 or more votes
- Looking for review articles/tutorials about understanding and interpreting phylogenetic trees the answers mostly point people to books. this is an excellent target for a tutorial.
- Is it possible to infer population genetics parameters like Ne using de-novo sequencing data of pooled samples? ultimately some good responses, but could be fleshed out more
- Why is maximum likelihood thought to be the best way to build phylogenetic tree?. the answers that have several votes seem short, or have explanations without citations. this might be a good candidate for a tutorial, reframed to address strengths and weaknesses of phylogenetic methods.
- How do I match orthologues in one species to another, genome scale? a bunch of different answers, not consolidated. this would be an excellent candidate for a tutorial.
- How can I compare rates of evolution for two sets of genes? this is a nice circumscribed evolutionary analysis problem. the answers call for putting together a pipeline. is there an out-of-the-box solution in R, for instance? could someone write a script for that as a hackathon target?
Some of these only have a few votes because the tags don't have a lot of questions
- alignment: Should I strip alignment columns before making a tree?
- homology: What's the best way to find human paralogs?
- mrbayes: Should I strip alignment columns before making a tree?
- Delete a node from newick tree answers in python, R and Perl. This would be nice for a tutorial?
- Where to get a mammalian phylogenetic tree with branch distances UGH! the answer is TimeTree (= NCBI taxonomy) someone should give a better answer.
- Concatenating nexus files (for MrBayes, etc)
- how to code multiple states for discrete data type this question is answered poorly. could be done much better.
- nexus: Where to find huge sample files? (Phylip, Nexus, ClustalW, etc) questioner is developing a parser and wants sample files to use for testing
- I would suggest to browse the tag cloud sorted by votes Some of these have thousands of views.
- [What is a good phylogenetic tree display program for large data sets?]
- [What phylogeny viewing software do you use?]
- Phylogenetic analysis the question here is just how "to build a good MSA and tree". The ansewrs provide some tutorial material
some other tag-clouds to browse:
BioStars questions that are really evolutionary questions
- The relationship between protein abundance and protein function explanation and some citations about patterns and possible evolutionary explanations.
- Bio-informatics results supporting ongoing evolution various answers to whether there are bioinfo results that support the general theory fo evolution