## Input file information
Sequence_File=./Sequences.txt
Sequence_Type=DNA

## Descriptor method
Method=Kmer;NAC;DNC;TNC;ENAC;binary;CKSNAP;NCP;ANF;PSTNPss;PSTNPds;EIIP;DAC;DCC;DACC;TAC;TCC;TACC;PseDNC;PseKNC;PCPseDNC;PCPseTNC;SCPseDNC;SCPseTNC
## parameters for nucleotide, protein and peptide descriptors
# Kmer, RCKmer & PseKNC
Kmer_Size=5

# ENAC, EAAC, EGAAC, 
Sliding_Window=3

# CKSNAP, CKSAAP, CKSAAGP, KSCTriad
K_Space=9

# Auto-Correlation, NMBroto, Geary, Moran, SOCNuber, QSOrder
Lag_Value=1

# Auto-Correlation, Pseudo nucleic acid composition, QSOrder, PAAC, APAAC
Weight_Value=0.1

# Auto-Correlation & Pseudo nucleic acid composition, PAAC, APAAC
Lamada_Value=1

# Auto-Correlation & Pseudo nucleic acid composition
Di-DNA-Phychem=Rise;Roll;Shift;Slide;Tilt;Twist
Tri-DNA-Phychem=Dnase I;Bendability (DNAse);Trinucleotide GC Content
Di-DNA-Phychem-default6=Bend;GC content;Stability;Protein induced deformability;Duplex stability:(freeenergy);Inclination;A-philicity;Base stacking;Bending stiffness;Lisser_BZ_transition;Melting Temperature
Di-RNA-Phychem=Rise (RNA);Roll (RNA);Shift (RNA);Slide (RNA);Tilt (RNA);Twist (RNA)
All_Property=False

# AAindex properties, NMBroto, Geary, Moran
AAindex=ANDN920101;ARGP820101;ARGP820102;ARGP820103;BEGF750101;BEGF750102;BEGF750103;BHAR880101

# PseKRAAC
PseKRAAC_Model=g-gap
Ktuple=2
GapLamada=2
RAACCluster1=2
RAACCluster2=2
RAACCluster3A=2
RAACCluster3B=2
RAACCluster4=5
RAACCluster5=2
RAACCluster6A=5
RAACCluster6B=5
RAACCluster6C=5
RAACCluster7=2
RAACCluster8=2
RAACCluster9=2
RAACCluster10=2
RAACCluster11=2
RAACCluster12=2
RAACCluster13=4
RAACCluster14=2
RAACCluster15=2
RAACCluster16=2

## output format
Output_Format=svm

## Clustering (available method: kmeans, hcluster, apc, dbscan, meanshift)
Clustering_Algorithm=kmeans
Kmean_Cluster_Number=2
# sample or feature
Clustering_Type=sample

## Feature Normalization (MinMax or ZScore)
Feature_Normalization_Algorithm=ZScore

## Feature selection (CHI2, Fscore, IG, MIC, pearsonr)
Feature_Selection_Algorithm=Fscore
Selected_Feature_Number=130

## Dimension reduction (pca, lda or tsne)
Dimension_Reduction_Algorithm=tsne
Dimension_Reduction_Number=3

## Model construction (SVM, RF, LR, KNN, MLP)
ML=SVM;LR;RF;KNN;MLP

# Parameters for SVM
Kernel=poly
Cost=
Gamma=
Auto_Opterimize=True

# RF
Tree_Number=125

# KNN
K_Nearest_Neighbour=5

# ANN
Hidden_Layer_Size=2;40

## K-fold Cross-Validation
Validation=5

## Ensemble learning
Ensemble=Yes
