Question: Create multiple sequence alignment and phylogenetic tree in R using ape and clustalw by following steps below: Install clutalw (depending you your OS) on your

Create multiple sequence alignment and phylogenetic tree in R using ape and clustalw by following steps below:

Install clutalw (depending you your OS) on your computer using http://www.clustal.org/clustal2/link

Open R. (all of the following steps will be implemented in R)

Set a working directory

Install package ape from your R session by typing:

install.packages("ape ")

Load ape package by typing

library("ape ")

Read accession numbers of sequences

Accesion Numbers and sequences

>NP_000509.1 hemoglobin subunit beta [Homo sapiens] MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN ALAHKYH

>NP_990820.1 hemoglobin subunit beta [Gallus gallus] MVHWTAEEKQLITGLWGKVNVAECGAEALARLLIVYPWTQRFFASFGNLSSPTAILGNPMVRAHGKKVLT SFGDAVKNLDNIKNTFSQLSELHCDKLHVDPENFRLLGDILIIVLAAHFSKDFTPECQAAWQKLVRVVAH ALARKYH

>NP_776342.1 hemoglobin subunit beta [Bos taurus] MLTAEEKAAVTAFWGKVKVDEVGGEALGRLLVVYPWTQRFFESFGDLSTADAVMNNPKVKAHGKKVLDSF SNGMKHLDDLKGTFAALSELHCDKLHVDPENFKLLGNVLVVVLARNFGKEFTPVLQADFQKVVAGVANAL AHRYH

>NP_001138313.1 hemoglobin subunit beta [Sus scrofa] MVHLSAEEKEAVLGLWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSNADAVMGNPKVKAHGKKVLQ SFSDGLKHLDNLKGTFAKLSELHCDQLHVDPENFRLLGNVIVVVLARRLGHDFNPNVQAAFQKVVAGVAN ALAHKYH

>NP_001157490.1 hemoglobin subunit beta [Equus caballus] MVQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLH SFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVAN ALAHKYH

>NP_001187948.1 hemoglobin subunit beta [Ictalurus punctatus] MVVWTDFERATIQDVFSKIDYESVGHQALSRCLVVYPWTQRYFGSFGNLYNAAAIIGNPKVAAHGLVVVR GLEKAAKNMDNIKAIYADLSVLHSEKLHVDPDNFKLLADCITIVIASVLGASFTAEVQAALQKFLAVVVS ALGKQYQ

>NP_001091117.1 hemoglobin subunit beta [Ovis aries] MLTAEEKAAVTGFWGKVKVDEVGAEALGRLLVVYPWTQRFFEHFGDLSSADAVMNNAKVKAHGKKVLDSF SNGVQHLDDLKGTFAQLSELHCDKLHVDPENFRLLGNVLVVVLARHHGSEFTPVLQAEFQKVVAGVANAL AHRYH

>NP_001270296.1 hemoglobin subunit beta [Macaca fascicularis] MVHLTPEEKNAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSSPDAVMGNPKVKAHGKKVLG AFSDGLNHLDNLKGTFAQLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVAN ALAHKYH

>NP_001157900.1 hemoglobin subunit beta [Macaca mulatta] MVHLTPEEKTAVTTLWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSPDAVMGNPKVKAHGKKVLG AFSDGLNHLDNLKGTFAQLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVAN ALAHKYH

>NP_001162318.1 hemoglobin subunit beta [Papio anubis] MVHLTPEEKNAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFDSFGDLSSPAAVMGNPKVKAHGKKVLG AFSDGLNHLDNLKGTFAQLSELHCDKLHVDPENFKLLGNVLVCVLAHHFGKEFTPQVQAAYQKVVAGVAN ALAHKYH

Save the result from step 6 as file

Run clustalw by typing:

system(paste('"path_to_YOUR_clustalw/clustalw2.exe" new.fas'))

Read alignment file (*aln) it should be in your working directory

Create phylogenetic tree using neighbor-joining method

Plot the tree

Submit copy of working R-code

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