Hello everyone!
Hope all of you doing great.
For my y-str project I wanted to do the phylogenetic analysis using mega. My input file is in .phy format (phylip format) which is the output of the McGee's Y- utility software. I was trying to use this in mega software but during file conversion from phylip to mega format was getting the error that: "there was a problem converting your file to the MEGA format. Error: Expected number of sites, no number found".
Please can you help me to overcome from this problem.
Here is the phylip file that I wanted to convert to mega format.
11
modal 0 3510 4320 4320 1560 1560 2820 3510 3510 2820 4320
M9890_J-L8 3510 0 6390 5280 4320 4320 4320 7860 3510 3510 6390
394465_J-M 4320 6390 0 2820 3510 5280 5280 3510 7860 4320 4320
69065_J-M2 4320 5280 2820 0 3510 5280 4320 5280 6390 4320 4320
394467_J-M 1560 4320 3510 3510 0 2160 2160 2820 4320 3510 4320
357617_J-Z 1560 4320 5280 5280 2160 0 2160 2820 4320 3510 5280
M7801_J-M2 2820 4320 5280 4320 2160 2160 0 2820 4320 5280 6390
M8031_J-FG 3510 7860 3510 5280 2820 2820 2820 0 7860 5280 6390
M9061_J-M2 3510 3510 7860 6390 4320 4320 4320 7860 0 3510 4320
235231_J-Z 2820 3510 4320 4320 3510 3510 5280 5280 3510 0 2820
M9060_J-M2 4320 6390 4320 4320 4320 5280 6390 6390 4320 2820 0
Thank you very much
•
written
by
arpitha.hebbar.g •
2 answers
The PHYLIP format requires two pieces of information at the top of each file: the number of individuals and the number of sites in the alignment. However, I'm not sure what kind of data you're working with. I would recommend making sure you know what a PHYLIP file is and what one looks like for what you want to do first.
Using R, it is very simple, Here is my R script.
library(readr)
dist1 <- read_table2("input_file_phylip_distance.txt", col_names = FALSE, skip = 1)
names1 <- dist1$X1
dist1 <- dist1[,-1]
dist1[upper.tri(dist1,diag=TRUE)] <- NA #lower.tri
lin1 <- paste0("#mega","\n","!Title: Concatenated Files;", "\n","!Format DataType=Distance DataFormat=LowerLeft;","\n", sep = '')
write.table(lin1,"new_distance1.meg", col.names = FALSE, row.names = FALSE,quote = FALSE)
write.table(paste('#',names1, sep = ''),"new_distance1.meg", sep="\t",append = TRUE, col.names = FALSE, row.names = FALSE,quote = FALSE)
write.table("\n","new_distance1.meg", sep="\t",append = TRUE, col.names = FALSE, row.names = FALSE,quote = FALSE)
write.table(mt,"new_distance1.meg", sep="\t", append = TRUE,col.names = FALSE, row.names = FALSE)
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