• ecceTERA

• Referenced in 6 articles [sw24891]
• undated, fully dated or partially dated species trees. The ecceTERA reconciliation model and algorithm generalize ... most published DTL parsimony algorithms for binary species trees and binary gene trees. Moreover, ecceTERA...

• TxT

• Referenced in 1 article [sw07679]
• binary gene tree and binary species tree Tree reconciliation approach to inferring the duplication history ... problems when input gene and species trees are non-binary. We present the first linear ... binary gene tree and a binary species tree that minimizes the gene loss cost under ... method for reconciling two non-binary trees, this algorithm has been implemented in a software...

• phytools

• Referenced in 14 articles [sw10003]
• phylogenetic analysis of comparative data from species. For example, the package includes functions for Bayesian ... rate of character evolution on the tree; fast Brownian motion simulation and simulation under several ... trait evolution; fitting a model of correlated binary trait evolution; locating the position...

• OCTAL

• Referenced in 2 articles [sw29609]
• contain all of the species of interest. As incomplete gene trees can impact downstream analyses ... completion of gene trees is desirable. Results: We introduce the Optimal Tree Completion problem ... problem that involves completing an unrooted binary tree (i.e., adding missing leaves ... minimize its distance from a reference tree on a superset of the leaves. We present...

• GATC

• Referenced in 1 article [sw29603]
• with a species tree to correct, a posteriori, errors in gene trees inferred from multiple ... GATC, a new algorithm for reconstructing a binary gene tree with branch length. GATC returns...

• GAP

• Referenced in 3189 articles [sw00320]
• GAP is a system for computational discrete algebra...

• Gerris

• Referenced in 344 articles [sw00341]
• Gerris is a Free Software program for the...

• gmp

• Referenced in 282 articles [sw00363]
• GMP is a free library for arbitrary precision...

• Magma

• Referenced in 3315 articles [sw00540]
• Computer algebra system (CAS). Magma is a large...

• Maple

• Referenced in 5373 articles [sw00545]
• The result of over 30 years of cutting...

• Mathematica

• Referenced in 6355 articles [sw00554]
• Almost any workflow involves computing results, and that...

• Matlab

• Referenced in 13544 articles [sw00558]
• MATLAB® is a high-level language and interactive...

• nauty

• Referenced in 609 articles [sw00611]
• graph-theoretic program NAUTY: nauty is a program...

• R

• Referenced in 9969 articles [sw00771]
• R is a language and environment for statistical...

• SageMath

• Referenced in 1994 articles [sw00825]
• Sage (SageMath) is free, open-source math software...

• SINGULAR

• Referenced in 1508 articles [sw00866]
• SINGULAR is a Computer Algebra system (CAS) for...

• TSPLIB

• Referenced in 698 articles [sw00983]
• TSPLIB is a library of sample instances for...

• Cayley

• Referenced in 131 articles [sw01053]
• An introduction to the Group Theory Language, Cayley...

• AUTO

• Referenced in 943 articles [sw01059]
• AUTO is a software for continuation and bifurcation...

• GLIM

• Referenced in 193 articles [sw01126]
• GLIM - a system for interactive fitting of generalized...