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--- buildingaphylogeny [2013/09/09 11:02]
anniearchambault
+++ buildingaphylogeny [2013/09/16 08:33] (current)
anniearchambault
@@ Line 47: / Line 47: @@
 **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: \\
@@ Line 57: / Line 58: @@
 I had success by typing: \\
 sudo ./prank -d=/Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.fasta \\
-The output file will be named output.best.fas . Open it in any sequence viewer. My favorite one is [[www.genious.com|Geneious]], but it is commercial. The SuiteMSA is free.
+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.
 in Windows, type: \\
@@ Line 104: / Line 108: @@
 sudo make install \\
 fsa /Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.fasta >/Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.mfa \\
+or, for numerous sequences:  \\
+fsa /Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.fasta >/Users/anniearchambault/Documents/learning_teaching/Alignment_and_phylogeny_building/Protea_Faurea_ITS_trnL_75seq.mfa --fast \\
 Only for this program, I have been unable to complete the installation, and I have used instead the webserver http://orangutan.math.berkeley.edu/fsa/ \\
@@ Line 189: / Line 194: @@
 http://qcbs.ca/wp-content/uploads/2013/06/PR10_Fabaceae_11seqs.txt \\
 http://qcbs.ca/wp-content/uploads/2013/06/Oxytropis_ITSsequences_84seq.txt \\
-http://qcbs.ca/wp-content/uploads/2013/07/Fungal_ITS_ref_NEW_sequence.txt
+http://qcbs.ca/wp-content/uploads/2013/09/Fungal_ITS_ref_sequence_nl.fasta_.txt
+++++ Files of already aligned sequences - for cheaters!  |
+http://qcbs.ca/wp-content/uploads/2013/09/Oxytropis_ITS_prank_output.best_.fas_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/Oxytropis_ITS_muscleout.afa_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_muscleout.afa_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_fsa.mfa_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_Prank_output.best_.fas_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_sate_test.marker001.PR10_Fabaceae_11seqs.aln_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/PR10_Fabaceae_clustal.fasta_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/Fungal_ITS_ref_sequence_nlMuscleout.afa_.txt \\
+http://qcbs.ca/wp-content/uploads/2013/09/SATE_test.marker001.Fungal_ITS_ref_sequence_nl.aln_.txt \\
+++++