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TMRS

• computes time to most recent substitution.
• [Software]

EMWER

• Estimate selection strength and dominance from time-course allele frequency data
• github

reactIDR

• github

Branco

• Calculates expectations of how about nucleotides evolutionarily conserved on a phylogenetic tree
• github
• data

SCOUP

• Estimate rates of cell differentiation and gene-wise transcriptional noise from single cell RNA-seq data
• https://github.com/hmatsu1226/SCOUP

ParasoR

• Predict globally consistent RNA secondary structures at transcriptomic scale using parallel computation
• https://github.com/carushi/ParasoR

Rtools

• Compute various features of RNA secondary structures from given RNA sequences
• http://rtools.cbrc.jp

CSP

• Remove erroneous SNP fragments from next generation sequencing data
• https://sites.google.com/site/hmatsu1226/software/csp

CapR

• Computes secondary-structure contexts for each site of an RNA sequence
• https://sites.google.com/site/fukunagatsu/software/capr

MixSIH

• Infers haplotype blocks from next generation sequencing data
• https://sites.google.com/site/hmatsu1226/software/mixsih

Rchange

• Computes changes of secondary structure energy and entropy in response to base mutations
• http://rtools.cbrc.jp

Rentropy

• Computes entropy of secondary structures

Fdur

• Computes sufficient statistics of evolutionary tree models

Raccess

• Computes accessibilities of secondary structures
• http://rtools.cbrc.jp

Rfold

• Computes base pairing probabilities for long RNA sequences
• http://www.ncrna.org/software/rfold

Murlet

• An RNA multiple alignment program
• https://www.ncrna.org/softwares/murlet

MccaskillMEA

• Predicts common RNA secondary structure from RNA multiple alignments