FASTA file with sequence alignment. For reference
see example file.
path_to_file_assocpair_csv_result
csv file with results from SeqFeatRs assocpair function.
For reference see example file.
path_to_file_nexus_tree
nexus file with tree data for the given sequence
alignment. For reference see example file.
save_name_csv
name of file to which results are saved in csv format.
threshold
threshold for the number of allowed occurrences of tips
in one branch.
Details
Uses the results from SeqFeatRs assocpair analysis and a generated tree
for the same sequences in nexus format
(for tree generation, e.g http://mafft.cbrc.jp/alignment/server/ can be used).
For every pair of amino acids the number of sequences with both amino acids
inside one branch is calculated.
If this number exceeds 'threshold' times the number of found associations, this
association is considered to be due to a founder effect.
Value
Input file with an added column with founder effect information.
Note
Only use files generated with SeqFeatRs assocpair or assoctuple.
Author(s)
Bettina Budeus
References
Mayr, Ernst (1954). "Change of genetic environment and evolution". In Julian Huxley.
Evolution as a Process. London: George Allen & Unwin. OCLC 974739
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(SeqFeatR)
Error in library(SeqFeatR) : there is no package called 'SeqFeatR'
Execution halted