SimPhy
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Cited in
(42)- BoundedCoalescent
- Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL
- Comparing methods for species tree estimation with gene duplication and loss
- Phylogenetic placement problem: a hyperbolic embedding approach
- DEPP
- The bounded coalescent model: conditioning a genealogy on a minimum root date
- TRACTION: fast non-parametric improvement of estimated gene trees
- STAG
- Comparative genomics on artificial life
- Genetree
- ReCombinatorics
- Polynomial-Time Statistical Estimation of Species Trees Under Gene Duplication and Loss
- Notung
- DupTree
- RNAmmer
- DendroPy
- ASTRID
- NINJA
- Phylo-MCOA
- TreeJuxtaposer
- phylodyn
- ASTRAL-II
- TOPD/FMTS
- INDELible
- iGTP
- MulRF
- FastMe
- phyloscanner
- FastRFS
- OCTAL
- TreeFix
- DEPP
- DynaDup
- SPhyR
- ALF
- Reversible polymorphism-aware phylogenetic models and their application to tree inference
- APPLES
- ASTRAL-Pro
- FastMulRFS
- Aevol
- PRANC
- Visualizing codon usage within and across genomes: concepts and tools
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