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[antonkulaga]

Not clear from the README what is the core difference from TreeExp, support of Chip-Seq data? I am currently doing multi-species comparisons of gene expressions and I want to understand what are the optimal packages

[jingwyang]

hi @antonkulaga , AnceTran was developed only for the method of ancestral inference based on either RNA-seq or ChIP-seq data. And TreeExp is for expression data only and has integrated the methods including

• pairwise expression distance estimation

• relative rate test for transcriptome evolution

• the strength of expression conservation estimation

• ancestral transcriptome inference

So I recommend TreeExp for your analysis, and your can read the [Tutorial] (https://jingwyang.github.io/TreeExp-Tutorial/) for reference.