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buildingaphylogeny [2013/09/12 12:30] anniearchambault |
buildingaphylogeny [2013/09/12 21:02] anniearchambault |
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| 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 | ||
| 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. | ||
