2
$\begingroup$

I am very new here. Please help me with my codes as am trying to draw multiple sequence alignment as tree suing ggtree package in R and i have following error.

library(tidyverse)
library(ggtree) 
library(seqinr)
tree = read.tree("get_result.nwk")
msaplot(p=ggtree(tree), fasta = "get_results", window=c(150, 175))

Error in inds:inde : NA/NaN argument
> msaplot(p=ggtree(tree) + geom_tiplab(align=TRUE), fasta = "get_result.fasta", offset = 5)
Error in inds:inde : NA/NaN argument

My data looks like

LN681202.1_Ralstonia_solanacearum_isolate RsBe2
TGCAAGTCGAACGGCAGCGGGGGTAGCTTGCTACCTGCCGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGCCCTGTAGTGGGGGATAACTAGTCGAAAGACTAGCTAATACCGCATACGACCTGAGGGTGAAAGTGGGGGACCGCAAGGCCTCATGCTATAGGAGCGGCCGATGTCTGATTAGCTAGTTGGTGGGGTAAAGGCCCACCAAGGCGACGATCAGTAGCTGGTCTGAGAGGACGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAATCGCTTCGGTTAATACCTGGAGTGGATGACGGTACCGGAAGAATAAGGACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTGTGCAAGACCGATGTGAAATCCCCGGGCTTAACCTGGGAATTGCATTGGTGACTGCACAGCTAGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGATAACACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTTGGGGATTCATTTCCTTAGTAACGTAGCTAACGCGTGAAGTTGA
MF179616.1_Kv-1
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MN725749.1_SA006
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MF183971.1_Klebsiella_sp._strain_Kv-2
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MT507217.1_Uyi23r
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MF183969.1_Kv-3
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MK929064.1_NM43TS4-1
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MF183973.1_Kv-4
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MN082125.1_IILSFPR619
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MF183974.1_Kv-5
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MK671348.1_1
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MF183970.1_Kv-6
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTCGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MF682957.1_BT3409
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTCGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MF183972.1_Kv-7
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTCGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MZ475068.1_Klebsiella_variicola_EMBL-1
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTCGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
MF373424.1_KV8
GCTCTCGGGTGACGAGCGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACCTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGTGGGGGACCTTCGGCCTCATGCCATCAGATGTGCCCAGATGGGATTAGCTGGTAGGTGGGGTAACGGCTCCCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCAACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAAATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGACTTTCAGCGGGGAGGAAGGCGGTGAGGTTAATAACCTCATCGATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCGTCAAGTCGGATGTGAAATCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGATAACCGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATG
KC853296.1_JM16
GCTCTCGGGTGACGAGCGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACCTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGTGGGGGACCTTCGGCCTCATGCCATCAGATGTGCCCAGATGGGATTAGCTGGTAGGTGGGGTAACGGCTCCCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCAACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAAATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGACTTTCAGCGGGGAGGAAGGCGGTGAGGTTAATAACCTTATCGATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCGTCAAGTCGGATGTGAAATCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCTCAGGTGCGAAAGCGTGGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGATAACCGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATG

The tree info looks like this

(((((MF183974.1_Kv-5:0.0000000001,
(MN082125.1_IILSFPR619:0.0000000001,
(MF183973.1_Kv-4:0.0000000001,
(MK929064.1_NM43TS4-1:0.0000000001,
(MF183969.1_Kv-3:0.0000000001,
(MT507217.1_Uyi23r:0.0000000001,
MF183971.1_Klebsiella_sp._strain_Kv-2:0.0000000001)0.0000000000:0.0000000001)
0.0000000000:0.0000000001)0.0000000000:0.0000000001)0.0000000000:0.0000000001)
0.0000000000:0.0000000001)0.0000000000:0.0000000001,
MK671348.1_1:0.0000000001)0.8360000000:0.0012113715,
(MZ475068.1_Klebsiella_variicola_EMBL-1:0.0000000001,
(MF183972.1_Kv-7:0.0000000001,
(MF682957.1_BT3409:0.0000000001,
MF183970.1_Kv-6:0.0000000001)
0.0000000000:0.0000000001)0.0000000000:0.0000000001)0.0000000000:0.0000000001)
0.0000000000:0.0012061821,
((MN725749.1_SA006:0.0000000001,
MF179616.1_Kv-1:0.0000000001)
0.0000000000:0.0000024449,
LN681202.1_Ralstonia_solanacearum_isolate_RsBe2:99.9997264606)
0.0000000000:0.0000002190)1.0000000000:4.9050549661,
KC853296.1_JM16:0.0012459932,
MF373424.1_KV8:0.0000028057);
$\endgroup$
0

1 Answer 1

1
$\begingroup$

Firstly, do check tree is not an empty object, i.e. it uploads the tree file. Secondly, check the path to the alignment is correct get_results. Normally an alignment file would be suffixed with the alignment format, e.g. get_results.fa.

The immediate thing that strikes me, if all the paths are correct and the file names is the alignment format supplied isn't fasta format.

If you replace the contents of the file get_results (not get_results.nwk - because that's your tree file, with the following (wait ... see Note and Note2 ) ...

    >LN681202.1_Ralstonia_solanacearum_isolate_RsBe2
TGCAAGTCGAACGGCAGCGGGGGTAGCTTGCTACCTGCCGGCGAGTGGCGAACGGGTGAGTAATACATCGGAACGTGCCCTGTAGTGGGGGATAACTAGTCGAAAGACTAGCTAATACCGCATACGACCTGAGGGTGAAAGTGGGGGACCGCAAGGCCTCATGCTATAGGAGCGGCCGATGTCTGATTAGCTAGTTGGTGGGGTAAAGGCCCACCAAGGCGACGATCAGTAGCTGGTCTGAGAGGACGATCAGCCACACTGGGACTGAGACACGGCCCAGACTCCTACGGGAGGCAGCAGTGGGGAATTTTGGACAATGGGGGCAACCCTGATCCAGCAATGCCGCGTGTGTGAAGAAGGCCTTCGGGTTGTAAAGCACTTTTGTCCGGAAAGAAATCGCTTCGGTTAATACCTGGAGTGGATGACGGTACCGGAAGAATAAGGACCGGCTAACTACGTGCCAGCAGCCGCGGTAATACGTAGGGTCCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGTGCGCAGGCGGTTGTGCAAGACCGATGTGAAATCCCCGGGCTTAACCTGGGAATTGCATTGGTGACTGCACAGCTAGAGTGTGTCAGAGGGAGGTAGAATTCCACGTGTAGCAGTGAAATGCGTAGAGATGTGGAGGAATACCGATGGCGAAGGCAGCCTCCTGGGATAACACTGACGCTCATGCACGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACGCCCTAAACGATGTCAACTAGTTGTTGGGGATTCATTTCCTTAGTAACGTAGCTAACGCGTGAAGTTGA
>MF179616.1_Kv-1
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
>MN725749.1_SA006
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTCCGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
>MF183971.1_Klebsiella_sp._strain_Kv-2
 GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC
>MT507217.1_Uyi23r
GGAATTACTGGGCGTAAAGCGCACGCAGGCGGTCTGTCAAGTCGGATGTGAAATCCCCGGGCTCAACCTGGGAACTGCATTCGAAACTGCAGGCTAGAGTCTTGTAGAGGGGGGTAGAATTCCAGGTGTAGCGGTGAAATGCGTAGAGATCTGGAGGAATACCGGTGGCGAAGGCGGCCCCCTGGACAAAGACTGACGCCAGGTGCGAAAGCGTGGGGAGCAAACAGGATTAGATACCCTGGTAGTCCACCTGTAAACGATGTCGATTTGGAGGTTGTGCCCTTGAGGCGTGGCTTCCGGAGCTACGTTAAATCGACCGCCTGGGGAGTACGGCCGCAAGGAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGAACGCGAAGAACCTTACCTGGTCTTGACATCCACAGAACTTTCCAGAGATGGATTGGTGCCTTCGGGAACTGTGAGACAGGTGCTGCATGGCTGTCGTCAGCTCGGTTGTGAAATGTTGGGTTAAGTCCCGCAACCGCAACCCTTATCCTTTGTTGCCAGCGGTTAGGCCGGGAACTCAAAGGAGACTGCAGTGATAAACTGGAGGAAGGTGGGGATGACGTCAAGTCATCATGGCCCTTACCCAGGGCTACACACGTGCTCAATGGCATATACAAAGAGAAGCGACCAGAGCAAGCGGACCTCATAAAGTATGTCGTAGTCGATTGGAGTCTGCAACTCGACTCCATGAAGTCGGAATCGCTAGTAATCGTAGATCAGAATGCTCGGTGAATACGTTCCCGGGCCTTGTACACACCGC

Also ....

  • Please remove ALL space after the taxa name both in the alignment file and the treefile (I've done it for you in the alignment file)
  • LN681202.1_Ralstonia_solanacearum_isolate RsBe2 - the space is a problem between the word isolate and RsBe2 ... please make sure in the treefile the space is replaced with a _ character.

The names in the treefile must exactly match the names in the alignment file. Just to confirm, the last alignment file you forwarded had more taxa (that space is still an issue BTW), however ...

  • Fasta format must start the taxa name with a > otherwise it will not recognise it.

I think thats the basic error and why its saying null because it can't parse the alignment file. Getting the treefile names precisely aligned with the alignment taxa names might be an issue.


Note My fasta alignment format still looks like a dogs dinner, I can't get the fasta format on the markdown language working ....

  1. fasta format there must be a carriage return between the taxa name and the sequence.
  2. the > must not have any spaces between the start of the line (unlike my version) until the > ... nor any spaces anywhere on the line ...
  3. Spaces within the taxa name could cause problems in Newick tree format (depends what program you've used).

Note2 The alignment I edited and the new alignment you just supplied (presumably complete) obviously can't be simply cut and paste as I originally thought, but you get the gist. Writing code is a much easier way to do phylogenetics because there's very little manual editing and parsers do everything for you.


In the tree file you've correctly named LN681202.1_Ralstonia_solanacearum_isolate_RsBe2, but the same name must in the alignment file. Generally taxa names don't use spaces and are replaced with _, in phylip format for example this causes mayhem with the parser.


Finally If thats all thats wrong it would be cool, I think they'll be more to get it working correctly.

$\endgroup$
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    $\begingroup$ yes thats what went wrong.. it resolved the issue.. thank you all for your response and help.. $\endgroup$ Aug 31, 2022 at 15:55
  • $\begingroup$ Thanks @ManasaK.G. for the feedback, glad its resolved. Could you kindly mark the question 'resolved' if this was the solution please? $\endgroup$
    – M__
    Aug 31, 2022 at 15:57
  • $\begingroup$ A separate question would be cool, if I can help I will. @ManasaK.G. . $\endgroup$
    – M__
    Aug 31, 2022 at 15:58

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