; This file contains a list of files containing position-specific
; scoring matrices (in transfac format). obtained from 3 different
; motif discovery algorithms: RSAT peak-motifs, MEME-chip, and
; HOMER. These files can be fed to matrix-clustering, which will build
; a hierarchical tree enabling to analyse the consistency and
; difference between motifs discovered by the respective programs.
;
; How to run the demo
;   make -f ${RSAT}/makefiles/matrix-clustering_demo.mk cluster_HOMER_MEME_RSAT_Oct4_motifs
; 
; matrix-clustering -v 2 -file_table $RSAT/public_html/demo_files/Multi_algorithms_analysis.tab -title 'Oct4 motifs from RSAT|MEME-ChIP|Homer' -lth Ncor 0.5 -lth cor 0.7 -lth w 5 -hclust_method average -label_in_tree name -metric_build_tree Ncor -return heatmap,align_consensus -o results/matrix-clustering_results/Oct4_RSAT_MEME_HOMER/average_linkage/Ncor0.4_cor0.6/Oct4_RSAT_MEME_HOMER
${RSAT}/public_html/demo_files/MEME_ChIP_Oct4_matrices.tf	tf	MEME_ChIP
${RSAT}/public_html/demo_files/Homer_l13_mis3_hyper_Oct4_matrices.tf	tf	HOMER
${RSAT}/public_html/demo_files/RSAT_peak-motifs_Oct4_matrices.tf	tf	RSAT_peak_motifs