Datasets, matrices and supplementary figure for QMaker

Pfam_datasets.zip: Pfam training and test sets which were used with QMaker.<br>Matrices-normalized.zip: Eight output matrices for LG, Pfam, Pfam-gb, Bird, Insect, Mammal, Plant, and Yeast datasets.<br>Figure S1_new.pdf: The performance of five matrices, i.e., Q.pfam, JTT, LG, WAG on five clade-specific datasets, i.e., Bird, Plant, Insect, Yeast Mammal.<br>Table S1 (Correlations).docx: Correlation values (1000x) between six new matrices and 20 existing matrices, upper half are correlations of frequencies, lower half are correlations of exchangeabilities.<br>sample_training_10alignments.zip, sample_training_10genes.zip: two small datasets and training scripts, one has 10 alignments (these alignments do not share species and are extracted from Pfam dataset, shoulf be trained with option -S), the other has 10 genes of a same species (extracting from Plant dataset, training with option -p). Each dataset will need ~30 mins training time on a 10-core machine.