Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
buildingaphylogeny [2013/09/12 21:02]
anniearchambault
buildingaphylogeny [2013/09/16 08:33]
anniearchambault
Line 47: Line 47:
  
 **PRANK** **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 \\  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: \\  In the terminal, change directory to where the compressed file is located. Uncompress by typing: \\ 
Line 58: Line 59:
 sudo ./prank -d=/​Users/​anniearchambault/​Documents/​learning_teaching/​Alignment_and_phylogeny_building/​Protea_Faurea_ITS_trnL_75seq.fasta \\  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: \\  For the Fungal_ITS_ref_sequence_nl.fasta_.txt,​ rename sequences with shorter names by typing this command: \\ 
-cut Fungal_ITS_ref_sequence_nl.fasta_.txt ​-f 1-3 -d ' ' > Fungal_ITS_ref_sequence_nl_trim.fasta+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.  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.