Usando o STRUCTURE

 structure_threader run -i Ugibba_filtered1_ref.vcf -o ./results2 -als ~/anaconda3/envs/structure/bin/alstructure_wrapper.R -K 15 -t 3 --ind Ugibba.indfile

Fonte: https://radcamp.github.io/Lisbon2020/05_POPULATION_STRUCTURE.html


Sendo que o arquivo ind:

The “indfile”

Open the file with your favorite text editor. If you don’t have one and want to stay on the CLI, you can try the command nano ~/str_analyses/oyster.indfile in a new terminal window. The first few lines of this file should look like this:

BC1_10_C6	Victoria_BC	4
BC1_20_C6	Victoria_BC	4
BC1_22_C7	Victoria_BC	4
BC1_4_C3	Victoria_BC	4
BC1_7_C5	Victoria_BC	4
BC1_8_C4	Victoria_BC	4
BC1_9_C5	Victoria_BC	4
BC2_10_C5	Klaskino_BC	1

Comentários

Postar um comentário

Postagens mais visitadas deste blog

Comandos comuns do PAUP - block

retirado de : http://www.peter.unmack.net/molecular/programs/paup.command.blocks.html Common PAUP analysis commands By Peter Unmack I usually paste the blocks below to the end of my nexus files, open the command line version (which runs faster than the GUI) and execute the file (I usually copy the datafile to my paup directory, or copy paup to where my datafile is).   Stuff highlighted in yellow is what usually gets changed by the user depending upon their dataset and needs. Parsimony Analysis begin paup; set autoclose=yes; set criterion=parsimony; set root=outgroup; set storebrlens=yes; set increase=auto; outgroup fish1 fish2 etc ; hsearch addseq=random nreps=1000 swap=tbr hold=1; savetrees file= datasetname .cb.pa.tree.nex format=altnex brlens=yes; pscores /tl ci ri rc; end; Parsimony Bootstrap Analysis begin paup; set autoclose=yes; set criterion=parsimony; set root=outgroup; set storebrlens=yes; set increase=auto; outgroup
Leia mais

Para instalar o StructRNAfinder

DOWNLOAD  and collaborate on StructRNAfinder development by accessing in our  GitHub account . All information to install and run it can be accessed there. Installing the stand-alone version:   (Only for linux) To see more details related to the installation process please see the INSTALL file. To install structRNAfinder and its requirements, type in a terminal located in structRNAfinder folder: sudo sh install.sh And follow the provided instructions. Pre-Requisites: StructRNAfinder uses third-part softwares and in-house Perl scripts in order to perform all its workflow. All them are automatically installed and configured when installing the tool. Bellow a list of softwares necessary to use it. Perl Linux perl library libgd-perl ( apt-get install libgd-perl ) Perl package  Bio::Graphics ( cpan install Bio::Graphics ) Infernal RNAfold  from  Vienna package Rfam  covariance models ( Version 12 ) As vezes tem que instalar o Bio::Graphics de novo depois, baixar  RFAM mais novo e dar o coma
Leia mais