Function reference

All functions

calc_similarity()

calculate similarity scores

create_distance_matrix()

Function to create a distance matrix

create_tree()

Function to generate a tree based on the distance matrix provided

dim_reduced_file

Example of how should be the output of a dimension reduced file

dim_reduction()

Function to perform dimension reduction

distance_matrix

Example of how should be the output of the distance matrix file

fasta fasta

Example of a small fasta file that can be used as input

get_alignment_score()

Function to perform pairwise alignment of all sequences and retrieve the alignment score

get_variance()

Function to get explained variance by each axis

kmeans_clustering()

Function to estimate optimal number of clusters and clustering using kmeans

kmeans_output

Example of kmeans_output

score_file

Example of score file

similarity_cluster()

Function to assess similarity within clusters

tcmuc_fasta tcmuc_fasta

Example of a complete fasta file that can be used as input