**FINDING SOFTWARE THAT IS NOT UNDER CONDA**

If you can not find software under CONDA environments, you could check in these places before to ask for an install:\\

   /opt/perun/bin/ 
   **Note: ** Some software here may be available directly in the environmental path, so it'll show up when you type: which software_name in the command line

   /scratch2/software/


**if you are a fan of iqtree:**\\
There are several versions of the program and you should use the specific builds for perun, it currently has installed versions:\\
   1.6.1 (/opt/perun/bin/iqtree-1.6.1-intel)
   1.5.5 (/opt/perun/bin/iqtree-omp-1.5.5-intel-build)
   these are builds that take advantage of the architecture of the cluster and perform task faster the the other 
   executables in any other directory

   if you use 1.5.5 then set this in your shell script
   source /scratch2/software/intel-build-2017/set-path



** if you are fan of BLAST or PLAST **\\

Blast and Plast use ncbi V4 formated databases: these must have been built with the flags **-parse_seqids -hash_index**):\\

To know the paths of the most updated databases for programs in this snippet click **[[databases_locations|]]**\\

1- the most updated version of **BLAST** in under conda\\
2- the most updated version of **PLAST** is available directly in the environmental path\\


** if you are fan of BLAT or LAST **\\

1- **BLAT** is available directly in the environmental path. To use it, you have to build a database. The simplest way is by typing this command:
   faToTwoBit in.fa out.2bit , where in.fa is your database_fastafile and out.2bit is the output_name
   then run the program:
   blat out.2but query_file -out=pslx [options] outputname.pslx

2- **LAST** is available at /scratch2/software/last-941/bin/\\
   Build a lastable database:
   lastdb [options] output-name fasta-sequence-file(s)
   then you are golden to use the executable that suits your needs
   
** if you are fan of DIAMOND/ac-DIAMOND, centrifuge or kraken-HLL**\\
All of these programs are under their own conda environment.

To know the paths of the most updated databases for programs in this snippet click **[[databases_locations|]]**\\