-s sequenceFileName  要处理的 phy 文件

-n outputFileName  输出的文件

-m substitutionModel  模型设定 方括号中的为可选项：

[-a weightFileName]  设定每个位点的权重，必须在同一文件夹中给出相应位点的权重

[-b bootstrapRandomNumberSeed]    设定 bootstrap 起始随机数

[-c numberOfCategories] 设定位点变化率的等级

[-d] -d 完全随机的搜索进化树，而不是从 maximum parsimony tree 开始。在 100 至 200 个分类单元间，该选可能会生成拓扑结构完全不同的局部最大似然树。

[-e likelihoodEpsilon]默认值为 0.1

[-E excludeFileName]  排除的位点文件名

[-f a|b|c|d|e|g|h|i|j|m|n|o|p|s|t|w|x] 算法

-f a rapid Bootstrap

-f b draw the bipartitions using a bunch of topologies

-f c checks if RAxML can read the alignment.

-f d rapid hill-climbing algorithm

-f e optimize the model parameters

-f g compute the per–site log Likelihoods for one ore more trees passed via -z.

-f h compute a log likelihood test (SH-test [21]) between a best tree passed via -t and a bunch of other trees passed via -z.

-f i performs a really thorough standard bootstrap

[-g groupingFileName]   预先分组的名称

[-h] program options

[-i initialRearrangementSetting] speccify an innitial rearrangement setting for the ininital phase of the search algorithm.

[-j]

[-k] optimize branchlength and model parameters on bootstrapped trees

[-l sequenceSimilarityThreshold]    Specify a threshold for sequence similarity clustering. [-L sequenceSimilarityThreshold]

[-M]   模型设定

-m GTRCAT: GTR approximation

-m GTRMIX: Search a good topology under GTRCAT

-m GTRGAMMA: General Time Reversible model of nucleotide subistution with the gamma model of rate heterogeneity.

-m GTRCAT_GAMMA:  Inference of the tree with site-specific evolutionary rates. 4 discrete GAMMA rates,

-m GTRGAMMAI: Same as GTRGAMMA, but with estimate of proportion of invariable sites

-m GTRMIXI: Same as GTRMIX, but with estimate of proportion of invariable sites.

-m GTRCAT GAMMAI: Same as GTRCAT_GAMMA, but with estimate of proportion of invariable sites.

-n outputFileName  输出文件名

-o outgroupName(s) 设定外类群  如果有两个以上外类群，两者之间不能用空格，而应该用英文的"," DNA, gen1=1-500 DNA, gen2=501-1000

[-p parsimonyRandomSeed] [-P proteinModel]

[-q multipleModelFileName]

-q multiple modelfile name

如将以下信息拷贝到另存为文件  genenames

DNA, rbcLa = 1-526

DNA, matK = 527-1472

调用方法  -q genenames

-m GTRGAMMA

[-r binaryConstraintTree]

-s sequenceFileName  待分析的 phy 文件

[-t userStartingTree]  用户指定的进化树拓扑结构

[-T numberOfThreads]

[-u multiBootstrapSearches] Specify the number of multiple BS searches per replicate to obtain better ML trees for each replicate. [-v] 版本信息

[-w workingDirectory] 将文件写入的工作目录

[-x rapidBootstrapRandomNumberSeed]    invoke rapidBootstrap

[-y] -y 只输出简约树拓扑结构，之后推出，该树也可以用于 GARLI 等软件

[-z multipleTreesFile]

[-#|-N numberOfRuns]

生成的文件

RAxML log.exampleRun:   运行时间、似然值/ number of checkpoint file

RAxML result.exampleRun:    树文件

RAxML info.exampleRun:    -m GTRGAMMA or -m GTRMIX contains information about the model and algorithm used

RAxML parsimonyTree.exampleRun: -t.

RAxML randomTree.exampleRun: -d.

RAxML checkpoint.exampleRun.checkpointNumber: -j

RAxML bootstrap.exampleRun: -# and -b or -x

RAxML bipartitions.exampleRun: -f b

RAxML reducedList.exampleRun: -l or -L

RAxML bipartitionFrequencies.exampleRun: -t , -z , -f m

RAxML perSiteLLs.exampleRun: -f g

RAxML bestTree.exampleRun: -x 12345 -f a

RAxML distances.exampleRun: -f x