Datasets, matrices and supplementary figure for QMaker

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dataset

posted on 2020-12-24, 09:06 authored by Cuong DangCuong Dang

Pfam_datasets.zip: Pfam training and test sets which were used with QMaker.

05_clades.zip: Training and test sets of five clades which were used with QMaker.

Matrices-normalized.zip: Eight output matrices for LG, Pfam, Pfam-gb, Bird, Insect, Mammal, Plant, and Yeast datasets.

Fig_A1.tiff: The performance of four matrices Q.pfam, JTT, LG, WAG on Pfam, Bird, Plant, Insect, Yeast, and Mammal datasets.

Fig_A2.tiff: The bubble plot show relative differences between amino acid exchangeability rates in Q.pfam and Q.yeast. The explanations as similar as in Figure 4.

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.

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.