Difference between revisions of "Software"

From MolEvol
(Alignment)
 
Line 1: Line 1:
 +
<span style="font-size:large;background-color:yellow;color:red;font-weight:bold">This is the OLD website: the NEW web site is at [https://molevolworkshop.github.io/ molevolworkshop.github.io]. Please go there for information about the 2020 Workshop.</span>
 +
 
==Alignment==
 
==Alignment==
 
*[https://ormbunkar.se/aliview/ AliView]
 
*[https://ormbunkar.se/aliview/ AliView]

Latest revision as of 15:48, 9 December 2019

This is the OLD website: the NEW web site is at molevolworkshop.github.io. Please go there for information about the 2020 Workshop.

Alignment

Phylogenetic tree building and analysis

Post-Hoc Tree Analysis or manipulation

  • DendroPy (Fantastic for summarizing posteriors, distance calculations, and simulation)
  • Newick Utilities (Rerooting and tree parsing from the command line)

Tree Viewing and Plotting

  • FigTree
  • ggTree (R package for producing publication-quality trees with metadata)

Other

Pipelines

  • Agalma (Transcriptome assembly and analysis)
  • ipyrad (RADseq data assembly and analysis)

Population analysis

Similarity searching