[[faq]]

Frequently Asked Questions

  • What similarity matrices does trimAl use?

    • trimAl uses, by default, the BLOSUM62 similarity matrix in proteins and the Identity matrix in DNA/RNA sequence alignments. However, the users can upload any other matrix of their choice (see below)
  • Can users define their own similarity matrices?

    • Yes. trimAl can use other similarity matrices defined by the user using the -matrix parameter.
  • What automated methods does trimAl have?

    • trimAl has 3 automated method: gappyout based on gaps information, strict and strictplus based on a combination between gap and similarity distribution. Moreover, trimAl has an heuristic method to decide which is the best automated method to apply a given alignment based on its features.
  • Are there any methods optimized for Neighbor Joining and Maximum Likelihood phylogenetic tree reconstruction?

    • In our benchmark which was done with protein simulated data, we have seen that the strictplus automated method works better for tree reconstruction using Neighbor Joining while the automated1 heuristic method works better for the tree reconstruction using Maximum Likelihood. However, the user should keep in mind that this has not been tested in real biological data nor using DNA/RNA data. trimAl has other methods -gappyout and strict- that may be better in other situations.
faq.txt ยท Last modified: 2009/06/11 09:23 by tgabaldon
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