系统发育常见软件与在线⼯具合集
本篇⽂章是为了记录本⼈在系统发育实验和数据分析过程中，所使⽤过的以及部分未使⽤但如雷贯⽿的软件的集合。当然，相对于整个系统发育软件之汪洋⼤海，此处不过⼀滴⽔！
1. 数据获取
1.1 测序数据整理
DNAstar DNAstar是⼀个序列编辑和分析的全功能包，其⼦包Seqman能⽐对和⼿动调整Sanger测序⽂件，操作简单，但默认不解析少量低质量测序结果的测序⽂件
Chromas 功能和Seqman类似，不⽀持测序结果反向互补查看，但没有Seqman的低质量限制，可做为Seqman的补充
1.2 序列⽐对
Mega 全能型系统发育⼯具，⽐对和编辑序列较⽅便，⽐对算法集成ClustralX和Muscle⽅法
Mafft 快速⽽准确的序列⽐对⼯具，在序列⽐对⽅⾯⽐Mega效果更好
1.3 ⽐对后处理
PhyDE 序列编辑软件，可以多开，⽅便多个⽐对结果之间进⾏⽐较
FastGap 可以对⽐对后的序列的gap进⾏重编码，提⾼序列信息使⽤效率
Gblocks 在线⼯具，选择序列保守区，使得后续系统发育分析免受变异过⼤的⽐对区域的不良影响
DAMBE ⼀个低调但全能的系统发育软件，定位与Mega类似，包括饱和度检测功能点
DNAsp 序列分析软件，计算各种序列多样性数据，如核苷酸多样性、序列信息位点含量、单倍型等
2. 格式转换
DAMBE 少有的集成有格式转换模块的综合性软件html网页设计的标题
PGDSpider 专门的格式转换软件，可以在众多系统发育和体遗传学的⽂件格式之间转换
EasyCodeML 进化选择压⼒检测软件，但是也集成了部分常见格式的转换功能
3. 模型选择
Modeltest/MrModeltest---ModelGUI 最常使⽤的DNA突变模型选择软件组合，依附于PAUP，直接⽣成适⽤于MrBayes和Garli的对应模型命令模块
jmodeltest 模型选择软件，优势是可选择的模型很多，缺点是运算速度很慢
Moderfinder 较新的模型选择软件，速度很快，集成于iqtree⾥⾯
PartitionFinder 较新的模型和数据分区选择软件
4. 发育树构建
4.1 最⼤简约法法
PAUP ⽼牌著名系统发育软件，⽀持UPGMA，MP，ML等⽅法。
Mega ⽀持最⼤简约法
DAMBE ⽀持最⼤简约法
Phylip ⽼牌系统发育软件，可覆盖系统发育构建的⼏乎全部流程
4.2 最⼤似然法
PAUP ⽼牌著名系统发育软件，⽀持UPGMA，MP，ML等⽅法。
Phylip ⽼牌系统发育软件，可覆盖系统发育构建的⼏乎全部流程
Garli 基于遗传算法的构建ML树的软件
RAxML 现在较为常⽤的ML树构建软件，速度很快，从RAxML开始，由于peusolikelihood和快速⾃展的引⼊，最⼤似然法的运算速度得到极⼤改善，⼀改最⼤似然法计算强度⼤的印象
ExaML RAxML的扩展，⽀持并⾏运算，速度较快，适⽤于基因组数据
iqtree 集成了模型选择和发育树评估的建树软件，使⽤起来⽅便，在Zhou et al.对各种快速似然发育树构建⽅法
（RAxML，PhyML，Fasttree，iqtree）的评价中，iqtree综合表现最好
Programs Optimal
ity
Criterio
n
Starting Tree
Topological
Moves
Supported
Models(DN
A)
Supported
Models(AA
)
Partitio
ned
Analysis
RAxML
v8.2.0 (ExaML v3.0.17)ML
Parsimony/random/
custom
SPR
Common
and custom
models
JC69, K80,
HKY85, GTR
Y
PhyML
v20160530ML
Parsimony/random/
custom
Interleaved NNI
and SPR
Common
php源码扫描
and custom
models
Common
and custom
models
Y
IQ-TREE v1.4.2ML
BIONJ and multiple
parsimony/random/
custom
NNI and
stochastic
perturbation
Common
and custom
models
Common
and custom
models
Y
FastTree v2.1.9ML Heuristic NJ
NNI and SPR
(ME) followed by
NNI (ML)
JTT, WAG,
LG
JC69, GTR N
图表参考⾃该论⽂
4.3 贝叶斯法
MrBayes 贝叶斯⽅法的主要软件，但相对于⽀持快速⾃展的ML⽅法，速度较慢
BEAST ⼀个基于贝叶斯⽅法构建发育树、物种树、时间树以及时空动态的平台型软件，分为两个版本BEAST1和BEAST2。
ExaBayes 针对于⼤数据集的贝叶斯构树软件
Pro
gra
m
Brief description
BEA ST Implements a vast number of models. Examples are the simultaneous estimation of the tree topology and divergence times, phylodynamics, phylogeography, and species tree estimation under the MSC model.
MrB aye s Implements a large number of models for analysis of nucleotide, amino acid and morphological data. Estimates species phylogenies and species divergence times.
Rev Bay es Similar to MrBayes, but with its own programming language to set up complex hierarchical Bayesian models.
MC
MC
Tre
e
Estimates divergence times on a fixed phylogenetic tree.
Phy cas Estimates phylogenetic trees based on nucleotide data. This allows for multifurcating trees, helping to reduce spuriously high posterior probabilities for phylogenies.
Phy loB aye s Reconstructs phylogenetic trees using infinite mixture models to account for among-site and among-lineage heterogeneity in nucleotide or amino acid compositions, which may be important for inferring deep phylogenies.
BPP Implements species tree estimation and species delimitation under the MSC model using multi-loci genomic sequence data.
Mig rate Estimates population sizes and migration rates under the population-subdivision model based on molecular data.
IMa 2Estimates divergence times, population sizes and migration rates under the isolation-with-migration model using multi-loci DNA sequence data and a fixed phylogenetic tree for populations.
Str
uct
ure
Estimates population structure from multi-loci genotype data.
BA
MM
Estimates clade diversification rates on phylogenies.
Tra
cer
A program for MCMC diagnostics and summaries.
AW TY A package for MCMC diagnostics for Bayesian phylogenetic inference.
Pro
gra
m
Brief description
图表参考⾃此论⽂
5. 系统发育⽹络构建
TCS 简单的构建系统发育⽹络的软件，官⽅的下载链接可能已经失效
web技术的应用领域Network 同上
SplitsTree ⽀持多种算法（距离法，NJ法等）的发育⽹络构建软件
Phylonet 利⽤最⼤似然算法推断系统发育⽹络，能够区分杂交事件和不完全谱系分选JML 同样宣称可以区分杂交和不完全谱系分选的发育⽹络构建软件
Dendroscope
SplitsTree
Net
work
Arlequin TCS T-Rex
Spectro
Net
Combi
neTree
s
Input format Nexus Uniq
ue
Unique, can
import Phylip
Nexus Phylip Nexus Nexus
feature动词的用法Data types Characters,
distances,
trees
Char
acter
s
Characters
Characters
, distances
Characters
, distances
Characte
rs, trees
Trees
Network method
Character-display
networks
Median network**
Qusai-median
network
**
Reduced-median
network
Greedily reduced-
median netword
Local buneman
graph
Quartet window
annlysis
Pruned median
文件格式转换appnetwork
Pruned quasi-
median network
*
Parsimony splits*
Splits
decomposition
*
Neighobor-net*
Parsimony
networks
Netting
Union of
maximum-
parsimony trees
*
Minimum-spanning
netword
**
Median-joining**
Statistical-
parsimony
*
Other networks
Pyramids
Statistical
geometry
Concordance tree
Netview
Reticulogram*
Tree-display
networks
Consensus
network
** Super-network*
Filtered super-network *
SplitsTree
Net
work
Arlequin TCS T-Rex
Spectro
Net
Combi
neTree
s
该表参考⾃书籍 Morrison, D. A. (2011). An introduction to phylogenetic networks. RJR productions.
6. 物种树构建
BEAST
BPP BEAST和BPP软件推算物种树的时候同时计算每个基因的基因树及其和每个物种树的组合概率，称为⼀步法，⼀般较为准确，但是运算量很⼤，难以适⽤于基因组时代的⼤量数据
ASTRAL 该软件需先计算出每个基因的基因树，然后再根据基因树利⽤溯祖原理推断出物种树，称为两步法，速度很快
STEM-hy
MP-EST
NJst
手机网页游戏怎么设置全屏Pro gra m Analytical
framework
Input Output
GM YC Best-fit tree branching
models (coalescent vs
Yule)
Ultrametric gene tree
Transition point from species to populations,
and estimate of species number
Bro wnie Maximum likelihood or
gene tree parsimony
Gene trees
Species tree of delimited species and group
membership
Spe deS TEM Maximum likelihood
and/or information
theory
Sequence alignments and
group membership
Species tree of delimited species
BP& P Bayesian and/or
reversible-jump MCMC
Sequence alignments,
group membership, and
guide tree
Posterior probability distribution of species
delimitation models, coalescent times, and
population sizes
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