• # HyDe

• Referenced in 2 articles [sw29663]
• producing a set of functions called phylogenetic invariants. In this article, we introduce HyDe ... software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization...
• # ProtTest 3

• Referenced in 4 articles [sw23032]
• maximum likelihood (ML) estimation of phylogenetic trees and model parameters. The current version of ProtTest ... consider rate variation among sites (+I: invariable sites; +G: gamma-distributed rates) and the observed...
• # GARLI

• Referenced in 1 article [sw29598]
• rapid likelihood inference. GARLI performs heuristic phylogenetic searches under the General Time Reversible (GTR) model ... distributed rate heterogeneity and a proportion of invariant sites. The implementation of this model...
• # CoMeta

• Referenced in 2 articles [sw25789]
• Comparison of metabolic pathways is useful in phylogenetic analysis and for understanding metabolic functions when ... pathways and comparing the corresponding $T$-invariant bases, which represent minimal subsets of reactions that...