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== AAF ==
== AAF ==
[[SW:GCATemplates|GCATemplates]] available: [https://github.tamu.edu/cmdickens/GCATemplates/blob/master/templates/ada/run_aaf_20160518_ada.sh ada]
[[SW:GCATemplates|GCATemplates]] available: [https://github.tamu.edu/cmdickens/GCATemplates/blob/master/templates/grace/run_aaf_20171001_grace.sh grace]
AAF [https://sourceforge.net/projects/aaf-phylogeny/ homepage]
AAF [https://sourceforge.net/projects/aaf-phylogeny/ homepage]

Latest revision as of 10:52, 8 July 2021


GCATemplates available: grace

AAF homepage

Use the module spider command to see the available versions of AAF:

 module spider AAF

AAF (alignment and assembly-free) is a free software package that reconstructs phylogeny from next-generation sequencing data without assembly and alignment.

It takes raw sequencing reads from each sample altogether and generates a distance matrix based on the proportion of shared k-mers between each sample and reconstruct a phylogeny based on the distance matrix.

If you are running aaf_distance.py with > 10 cores and the command is failing with a message like IndexError: list index out of range then use fewer cores such as -t 5