Sankoff is a fast and parallel implementation for ancestral state reconstruction based on Sankoff's algorithm

Installation

Conda installation (Linux and Mac): (Generated based on README from CRISPRme)

• Open a terminal window
• Paste this command into the terminal:

  curl https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh --output Miniconda3-latest-Linux-x86_64.sh
  

• If the file is correctly downloaded you now need to execute it to complete the installation, so paste this command into the terminal:
  • Linux

  bash Miniconda3-latest-Linux-x86_64.sh
  

• Press ENTER when requested and yes when an answer is requested, in this way you allow conda to set all the directories in your HOME path for an easy use
• After the complete installation you will receive this message “Thank you for installing Miniconda3!” to certify the correct installation.
• Now you need to close the terminal window you are using and open a new one, to allow the system to start conda.
• In the new terminal window you should see something like this:

  (base) user@computer:~$
  

  If you read the "(base)" like this, conda is loaded correctly and you can start using it.
• Now, you can install sankoff by typing the command:

  conda install -c bioconda sankoff
  

• To test your installation, type the command:

  sankoff --help
  

• After the execution of the command you should see sankoff options.

Now the software is installed and ready to be used.

Usage

An easy usage could be as follows

sankoff --tree [TREE-FILE] --aln [INPUT-SEQUENCE-FILE] --cost [COST-MATRIX-FILE] --out-as [ANCESTRAL-STATE-OUTPUT-FILE]

Sankoff with the above parameters reads the tree from TREE-FILE and leaf node sequences from INPUT-SEQUENCE-FILE as well as cost matrix from file COST-MATRIX-FILE, executes the sankoff algorithm and prints sequence for leaf nodes and internal nodes to file ANCESTRAL-STATE-OUTPUT-FILE. If internal nodes are unnamed, option --ilabel [PREFIX] could be used which assigns label to internal nodes with prefix PREFIX. Then the tree with new names could be saved with option --out-tree [OUT-TREE] in file OUT-TREE.

Example

• Download leaf node sequences from aln.txt and save as aln1.txt
• Download cost matrix from cost-1.txt and save as cost-1.txt
• Download input phylogeny from tree1.txt and save as cost-1.txt
• Run

sankoff --tree tree1.txt --aln aln.txt --cost cost-1.txt --ilabel inode --out-as aln-out.txt --out-tree tree-out.txt

• Internal nodes of the input tree is now labled and the tree is saved in tree-out.txt.
• Sequence infered for internal nodes as well as sequence for leaf nodes are saved in aln-out.txt.

Options

• --help: Prints help.
• --tree [TREE-FILE]: Input phylogeny in the plain tree format.
• --nexus [TREE-FILE]: Input phylogeny in the nexus format.
• --aln [INPUT-SEQUENCE-FILE]: Input sequences for leaf nodes.
• --cost [COST-MATRIX-FILE]: File containing the cost matrix. First row and first column represent characters in the sequence files. Values are integer.
• --cost-identity-aa [identical] [non-identical] [X-AA] [X-X] [X-GAP] [AA-GAP] [GAP-GAP]: Instead of cost matrix, this option may be used. This option builds a cost matrix for amino acids with two special characters: gap (-) and unknown (X). The matrix is filled with the parameters given to this option.
• --cost-identity-dna [identical] [non-identical] [X-NA] [X-X] [X-GAP] [NA-GAP] [GAP-GAP]: Instead of cost matrix, this option may be used. This option builds a cost matrix for DNA with two special characters: gap (-) and unknown (X). The matrix is filled with the parameters given to this option.
• --ilabel [PREFIX]: If present, internal nodes are labeled with [PREFIX]#NUM where #NUM will be different values.
• --out-tree [OUT-TREE]: The phylogeny, potentially after labeling, will be saved in this file.
• --out-as [ANCESTRAL-STATE-OUTPUT-FILE]: Output file containing all the sequences for internal nodes as well as leaf nodes.
• --nthread [THREAD-COUNT]: Use THREAD-COUNT threads for execution.
• --induce_tree_over_samples: Remove samples from the tree which are not present in the sequence file and rebuild the tree.

Contributors

• Mohammad-Hadi Foroughmand-Araabi
• Sama Goliaei

License

This project is under GPL 3.0 license.