foundereffectfinder: Tries to identify a founder effect in results from SeqFeatRs...
In SeqFeatR: A Tool to Associate FASTA Sequences and Features

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Takes the result of co-mutation analysis like SeqFeatRs assocpair function and adds a column with a note if the row is in the same branch.

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foundereffectfinder(path_to_file_sequence_alignment = NULL,
    path_to_file_assocpair_csv_result = NULL, path_to_file_nexus_tree = NULL,
    save_name_csv, threshold = 7)

`path_to_file_sequence_alignment`	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.

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.

Input file with an added column with founder effect information.

Only use files generated with SeqFeatRs assocpair or assoctuple.

Bettina Budeus

Mayr, Ernst (1954). "Change of genetic environment and evolution". In Julian Huxley. Evolution as a Process. London: George Allen & Unwin. OCLC 974739

assocpair

#Input files
fasta_input <- system.file("extdata", "Example_aa.fasta", package="SeqFeatR")
assocpair_result <- system.file("extdata", "assocpair_results.csv", package="SeqFeatR")
tree_input <- system.file("extdata", "Example_tree.nh", package="SeqFeatR")

#Usage
foundereffectfinder(
	path_to_file_sequence_alignment=fasta_input,
	path_to_file_assocpair_csv_result=assocpair_result,
	path_to_file_nexus_tree=tree_input,
	save_name_csv="foundereffectfinder_result.csv",
	threshold=7)