Cipres  是一个网上服务器，可以提供很多的phylogenetic analysis tools. 类似于phylemon平台

linking:http://www.phylo.org/index.php/portal/

以下是他提供的各种计算服务：

• BEAST on XSEDE (1.7.4) - Bayesian Evolutionary Analysis by Sampling Trees - run on XSEDE
• Boxshade (3.31) - Pretty printing of aligned PS or DS
• Clearcut (1.0.9) - Fast Implementation of Relaxed Neighbor Joining
• ClustalW (1.82) - Create Multiple Alignments from Sequences
• Consense (Phylip 3.66) - Find A Consensus Tree
• CONTRAlign (2.01) - CONditional TRAining for Sequence Alignment
• Drawgram (Phylip 3.66) - Plots a cladogram- or phenogram- rooted tree
• Drawtree (Phylip 3.66) - Plots an unrooted tree diagram
• Format Validator (1.0) - Format Validation Tool
• FSA (1.15.0) - Distance-based alignment of DNA, RNA and proteins.
• GARLI 2.0 on XSEDE(Beta) (2.0) - Genetic Algorithm for Rapid Likelihood Inference - run on XSEDE.
• GARLI.conf Creator (2.0) - Creates a Garli.conf file for up to five partitions
• GARLI on XSEDE (1.0) - Genetic Algorithm for Rapid Likelihood Inference - run on teragrid.
• MAFFT on TG (6.822) - Multiple alignment program for amino acid or nucleotide sequences; parallel version
• MrBayes on XSEDE (3.1.2) - Tree Inference Using Bayesian Analysis - run on XSEDE
• MrBayes 3.2.1 (BETA) on XSEDE (3.2.1) - Tree Inference Using Bayesian Analysis - run on XSEDE
• MrBayes 3.2.1 Restart (BETA) on XSEDE Restart (3.2.1) - Tree Inference Using Bayesian Analysis - run on XSEDE
• Muscle (3.7) - Create Multiple Alignments from Sequences or Profiles
• MView_Alig (1.41.10) - Multiple Alignment Viewer
• NCLconverter (2.1) - A file format transformation tool
• PAUPRat (Not specified) - Parsimony ratchet searches using PAUP*
• POY (4.1.2) - Phylogenetic tree inference using dynamic homologies.
• Probalign (1.3) - Multiple sequence alignment using partition function posterior probabilities.
• ProbCons (1.12) - Probabilistic Consistency-based Multiple Alignment of Amino/Nucleic Acid Sequences
• RAxML-HPC BlackBox (7.3.2) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping on XSEDE.
• RAxML-HPC2 on XSEDE (7.3.2) - Phylogenetic tree inference using maximum likelihood/rapid bootstrapping run on XSEDE
• RAxML Light on XSEDE (BETA) (1.0.9) - RAxML-Light is a modification of RAxML for inferring very large trees on XSEDE machines
• Readseq (2.2) - Readseq: biological sequence format interconversion utility
• Seqboot (Phylip 3.66) - Bootstrap, Jackknife, or Permutation Resampling
• Seqretsplit (Emboss 6.0.0) - Split a multiple sequences file into many files, each containing one sequence

附件是做RAxML运算时提供的参数选择和相关说明