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--- buildingaphylogeny [2013/09/12 12:30]
anniearchambault
+++ buildingaphylogeny [2013/09/16 08:33] (current)
anniearchambault
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 **PRANK**
-Löytynoja, A., and N. Goldman. 2010. [[http://www.biomedcentral.com/1471-2105/11/579/abstract|webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser]]. BMC Bioinformatics 11: 579.
+Löytynoja, A., and N. Goldman. 2010. [[http://www.biomedcentral.com/1471-2105/11/579/abstract|webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser]]. BMC Bioinformatics 11: 579.  \\
+Löytynoja, A., and N. Goldman. 2005. [[http://www.pnas.org/content/102/30/10557|An algorithm for progressive multiple alignment of sequences with insertions]]. Proceedings of the National Academy of Sciences of the United States of America 102: 10557–10562 \\
 Dowload the program http://code.google.com/p/prank-msa/downloads/list. The README is here http://code.google.com/p/prank-msa/wiki/PRANK?tm=6 \\
 In the terminal, change directory to where the compressed file is located. Uncompress by typing: \\
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 sudo ./prank -d=/Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.fasta \\
 For the Fungal_ITS_ref_sequence_nl.fasta_.txt, rename sequences with shorter names by typing this command: \\
+cut  -f 1-3 -d ' ' Fungal_ITS_ref_sequence_nl.fasta_.txt > Fungal_ITS_ref_sequence_nl_trim.fasta
 The output file will be named output.best.fas . Open it in any sequence viewer. My favorite one is [[http://www.genious.com|Geneious]], but it is commercial. JalView is free.