ATGC: Replacement Matrix

Maximum likelihood estimation of amino acid replacement rate matrix

Cuong Cao Dang, Vincent Lefort, Vinh Sy Le, Quang Si Le, and Olivier Gascuel.

Bioinformatics. 2011, 27(19):2758-60.

The bootstrap procedure was run on:

The Pfam dataset used to infer the LG matrix (3912 alignments).
On this dataset, we ran:
- 20 bootstraps with 10 replicates each.
- 1 bootsrap with 500 replicates.
A subset of 100 randomly selected alignments from the dataset used to infer the FLU matrix.
On this dataset, we ran:
- 20 bootstraps with 10 replicates each.
- 1 bootstrap with 1000 replicates.

Results are compiled into this Excel sheet.