Example of Multiple sequence Alignment

>1ymg_A THE CHANNEL ARCHITE SASFWRAICAEFFASLFYVFFGLGASLRW-----AG------P---------lHVLQVAL AFGLALATLVQAVGHISGAHVNPAVTFAFLVGSQMSLLRAICYMVAQLLGAVAGAAVLYS VT--PPAvRGNlALNTLHPGVSVGQATIVEIFLTLQFVLCIFATYDERRNGRLGSVALAV GFSLTLGHLFGMYYTGAGMNPARSFAPAILTR------NFTNHWVYWVGPVIGAGLGSLL YDFLLFPRLKSVSERLSILKG
>2d57_A DOUBLE LAYERED 2D C TQAFWKAVTAEFLAMLIFVLLSVGSTINW-----GG-SENPLP---------VDMVLISL CFGLSIATMVQCFGHISGGHINPAVTVAMVCTRKISIAKSVFYITAQCLGAIIGAGILYL VT--PPSVVGGLGVTTVHGNLTAGHGLLVELIITFQLVFTIFASCDSKRTDVTGSVALAI GFSVAIGHLFAINYTGASMNPARSFGPAVIMG------NWENHWIYwVGPIIGAVLAGAL YEYVF--------------CP
>2f2b_A CRYSTAL STRUCTURE O MVSLTKRCIAEFIGTFILVFFGAGSAAVTLMIASGGTSPNPFNIGIGLLGGLGDWVAIGL AFGFAIAASIYALGNISGCHINPAVTIGLWSVKKFPGREVVPYIIAQLLGAAFGSFIFLQ CAGIGAATVGGLGATAPFPGISYWQAMLAEVVGTFLLMITIMGIAvDERAP-KGFAGIII GLTVAGIITTLGNISGSSLNPARTFGPYLNDMifagtDlWNYYSIYvIGPIVGAVLAALT YQYL---------------TS

library(seqinr) #load seqinr package
myseqs <- read.alignment("msa.fasta", format = "fasta")
mat <- dist.alignment(myseqs, matrix = "identity")
mat

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