Pairwise alignment score below the minimum limit. Guidetree failed. Exiting.

GoogleCodeExporter commented 9 years ago

Prank (v.111130) now return the error above for many sequence blocks.

Original issue reported on code.google.com by douglas....@gmail.com on 8 Feb 2012 at 11:01

GoogleCodeExporter commented 9 years ago

PRANK now uses Exonerate to anchor the alignment and speed up the computation. 
The error indicates that the anchoring has failed and the alignment produced is 
invalid. In order to resolve the issue, I would need an example data set that 
produces the error. Can you please send one?

One should be able to avoid the error with option "-noanchors" that disables 
the use of Exonerate. 

Alternatively one can use some other method to estimate the guide tree and then 
call PRANK only for the multiple alignment. One option is to use MAFFT like 
this:

mafft input_file.fas > mafft_alignment.fas

prank -njtree -d=mafft_alignment.fas -o=prank_alignment [other paramters]

This will estimate an NJ-tree from the MAFFT alignment, remove the gap signs 
and re-align the sequences. (Even better would be to use an ML method such as 
RAxML for the tree estimation.)

Original comment by ari.loyt...@gmail.com on 7 May 2012 at 12:24

GoogleCodeExporter commented 9 years ago

This should be fixed in the current version. PRANK now uses a MAFFT alignment 
for the initial guide tree estimation and doesn't attempt to make pairwise 
alignments.

Original comment by ari.loyt...@gmail.com on 12 Mar 2014 at 7:14

Changed state: Fixed

ariloytynoja / prank-msa

Pairwise alignment score below the minimum limit. Guidetree failed. Exiting. #1