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All base stochastic matrices used in this work
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* 9 Existing matrices: 

PAM
JTT
BLOSUM62 (coming under BLOSUM directory)
JOverington
WAG
VTML
LG
MIQS
PFASUM60 (coming under PFASUM directory)

* 6 inferred matrices (coming under MML directory)

MML_HOMSTRAD (HOMSTRAD database)
MML_Mattbench (Mattbench database)
MML_SABMARK-TWI (SABMARK Twilight Zone)
MML_SABMARK-SUP (SABMARK Superfamily)
MML_SCOP1 (sampled pairs from SCOP, aligned using DALI)
MML_SCOP2 (sampled pairs from SCOP, aligned using MMLigner)

* Additional: Base stochastic matrices derived for BLOSUM series (see BLOSUM directory) and PFASUM series (see PFASUM directory)



