Beginners Guide

Getting started with BuddySuite

This guide assumes you have already installed BuddySuite.

You can print a help file for each module with the -h flag:

$: seqbuddy -h
$: alignbuddy -h
$: phylobuddy -h
$: databasebuddy -h
$: buddysuite -h

This will list all of the available functions and some basic usage instructions. For a more detailed descriptions of any particular function, please refer to the appropriate wiki page.

It is highly recommend that you create short-form aliases or sym-links for each buddysuite tool, because it makes it much quicker to call the programs from the terminal window. The following short-forms are used throughout the wiki pages:

• sb (seqbuddy)
• alb (alignbuddy)
• pb (phylobuddy)
• db (databasebuddy)

Check that these commands are not currently used in your system path:

$: which sb alb pb db

If they are free (i.e., nothing is returned, or there is a note saying "command not found"), then simply copy the following into the .profile or .bashrc file in your root (usually ~/) directory:

alias sb="seqbuddy"
alias alb="alignbuddy"
alias pb="phylobuddy"
alias db="databasebuddy"

If there is a conflict, just select something else that makes sense to you.

##Usage Examples The BuddySuite modules are used in the following fashion:

$: sb "path to file" <command> <arguments>

For instance, the command

$: sb Mnemiopsis_cds.fa -tr

will take DNA sequences from Mnemiopsis_cds.fa and translate them to amino acid sequences, outputting the results to the terminal window.

To save the output to a file, use the unix redirect operator:

$: sb Mnemiopsis_cds.fa -tr > Mnemiopsis_pep.fa

You could than calculate the molecular weight of the newly translated sequence file with the -mw flag:

$: sb Mnemiopsis_pep.fa -mw

Although, if you do not require the intermediate protein sequences, you can simply pipe the information from one seqbuddy call into another using the '|' character:

$: sb Mnemiopsis_cds.fa -tr | sb -mw

By chaining commands and tools using pipes, you can build sophisticated pipelines without worrying about format conversion or storing unnecessary intermediate files:

$: sb Mnemiopsis_cds.fa -tr | alb -ga clustalo | alb -trm gappyout | pb -gt raxml -o nex > Mnemiopsis_tree.nex

The previous sequence of commands uses SeqBuddy to translate DNA sequences into amino acid sequences; AlignBuddy to generate a multiple sequence alignment with ClustalOmega and then clean that alignment with the gappy-out algorithm (originally popularized by trimAl); and PhyloBuddy to infer a phylogenetic tree with RAxML. The final tree is then converted to the nexus format with the -o (out_format) flag and redirected to a file.

For a complete listing of all the available BuddySuite functions, please refer to the appropriate wiki pages.