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Gblocks
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Select conservative blocks from multiple alignments for phylogenetic analysis
Gblocks (Linux, windows and web version)
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DAMBE
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Nucleotide substitution saturation detection
There are certain prerequisites for building a tree, for example: for nucleotide sequences, the most important one is the test of substitution saturation. If the sequence used to build a tree has become saturated, there is no need to build a tree.
DAMBE is a tool used for saturation testing.
DAMBE （windows，Linux versions）
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Asatura
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Amino acid saturation test
Asatura.rar 0.2MB （Fangluan Gao）
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jModelTest
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Nucleotide substitution model selection
jmodeltest-2.1.7-win.tar.gz （9.2MB）
jModelTest v2.1.10
jModelTest 2.1.10 Full release (tar.gz)
jModelTest 2.1.10 Manual (pdf)
ModelTest-NG: A New and Scalable Tool for the Selection of ...
ModelTest-NG
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ModelFinder
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ModelFinder
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modelgenerator
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Nucleotide and amino acid substitution model selection tools
modelgenerator_v_851.zip0.8MB （Fangluan Gao）
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modeltest
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Nucleotide model selection (48 methods)
modeltest3.7.zip0.9MB
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MrModeltest
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Nucleotide model selection (24 types)
MrModeltest2.3.zip0.5MB
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MrMTgui
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Evolutionary model selection tool
It integrates PAUP, modeltest and MrModeltest into a graphical tool.
mrmtgui.zip 4.6MB （Fangluan Gao）
Use diagrams to explain the selection of nucleotide substitution models – using MrMTgui
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PAUP
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PAUP 4.0 4.0b10 S[ecial Version
paupwin32_4b.rar1.3MB
PAUP4Registered version (Classic)
PAUP instructions
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MEGA-X
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MEGA-X
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RAxML
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RAxML || RAxML v8.2.X Manual
RAxML version 8
Using RAxML to build a maximum likelihood evolution tree (in Chinese)
Constructing Phylogenetic Tree with Online RaxML ( in Chinese) |
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BEAST2
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BEAST2 || online manual of BEAST2
Tutorials (see this)
Differentiation time analysis—beast2 software introduction (in Chinese)
Analysis of differentiation time based on beast2 software (in Chinese)
Introduction to BEAST2
BEAST Analisys FAQ (in Chinese)
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FigTree
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FigTree || Constructing a columnar evolutionary tree with FigTree ( in Chinese)
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TempEst
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TempEst || TempEst paper
RDP4 | Instruction | RDP4 Instruction Manual
Evolview ||Beautify the evolution tree with evolview (in Chinese)
Using Evolview to beautify the evolution tree tutorial and how to use it (Chinese)
advanced use of Evolview (in Chinese)
PhyML 3.0 || Mesquite
DnaSP ||
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IQ-TREE
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Documentation
IQ-TREE Tutorials and Manual in one PDF
IQ-TREE的使用 - 超快速用极大似然法构建进化树
使用IQ-TREE构建系统进化树
新一代建树工具IQ-Tree介绍
基于ML法重建系统发育树-IQ-TREE篇
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SimPlot
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Graphical analysis and analysis of genetic recombination tutorial (Simplot) ( in Chinese)
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Arlequin
Free Phylogenetic Network Software
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TimeTree
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TimeTree || Original article
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PAML
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paml
PAML Manual (pamlDOC.pdf) || || PAML FAQs (pamlFAQs.pdf)
PAML一般使用操作 || || PAML中文手册 || || PAML-中文说明
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