In some cases, it will be best to perform commands separately and check the output before continuing. For more repetitive tasks however, it can be useful to combine different commands and/or programs into a single command: a pipeline. This can be done by using the && separator between commands. This instructs Linux to execute the commands in series and only continues after the previous command was succesful, meaning that it will stop all combined commands when an error occurs. The below examples assume that your instance has the full PhylOStack installed. Keep in mind that you need to check the names of the in- and output files, as well as number of cores to be used and other parameters in each command.

Example 1: combining a RAxML based PartitionFinder analysis and Exabayes:

partitionfinder . --raxml && grep 'DNA,*' analysis/best_scheme.txt > partitions.txt && mpirun -np 8 exabayes -f alignment.phy -m DNA -c config.nex -q partitions.txt -n myrun -s 123 -R 2 > screenoutput.log && consense -f ExaBayes_topologies.myrun.0 -n myCons0

Example 2: combining an RAxML best tree analysis with multiparametric bootstrap support and RogueNaRok rogue taxon selection:

raxmlHPC -D -p 1234 -s alignment.phy -q partitions.txt -m GTRCAT -U -T 8 -n Best > STDOUT.Best.log && raxmlHPC -b 1234 -D -p 1324 -s alignment.phy -q partitions.txt -# autoMRE -m GTRCAT -U -T 8 -n Bootstraps > STDOUT.Bootstraps.log && raxmlHPC -f b -t RAxML_bestTree.Best -z RAxML_bootstrap.Bootstraps -m GTRCAT -T 8 -n BestBS > STDOUT.BestBS.log && RNR -i RAxML_bootstrap.Bootstraps -c 50 -T 8 -n MR50