Announcement (2016-10-01):
To fulfill the requirements of different Axiom SNP arrays and laboratories, we can provide customized reference databases of ALICE for you. If you have the need, please email Dr. Hsin-Chou Yang (hsinchou@stat.sinica.edu.tw). 


Introduction:
ALICE (AF/LOH/LCSH/AI/CNV/CNA Enterprise) is user-friendly software for an integrated analysis of allele frequency (AF), allelic imbalance (AI), loss of heterozygosity (LOH), long contiguous stretch of homozygosity (LCSH), and copy number variation or alteration (CNV/CNA) on the basis of SNP probe hybridization intensities and genotypes. The software, user manual, library files for APT, annotation files, test examples, and reference databases can be downloaded below.

 

Reference (* correspondence author):

Mei-Chu Huang, Tze-Po Tsuang, Chien-Hsiun Chen, Jer-Yuarn Wu, Yuan-Tsong Chen, Ling-Hui Li*, and Hsin-Chou Yang* (2015)

An Integrated Analysis Tool for Analyzing Hybridization Intensities and Genotypes Using New-Generation Population-Optimized Human Arrays. BMC Genomics 17:266. (http://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2478-8)

 

Contact:

Please kindly acknowledge if you have downloaded ALICE. We will inform you the update of ALICE. Any questions, comments and suggestions on ALICE are welcome. Please send your feedback to hsinchou@stat.sinica.edu.tw.

 

Download software & user manual:

Version

Content

Screen resolution

Architecture

Size

Update date

ALICE v. 1.0 Software Width < 800 32-bit 164 MB 2015/10/04
64-bit 164 MB 2015/10/04
Width ≥ 800 32-bit 164 MB 2015/10/04
64-bit 164 MB 2015/10/04
User manual - a brief guide for running a default example in ALICE 1.07 MB 2015/10/04
User manual - a full guide for all functions in ALICE 5.30 MB 2015/10/04
Frequently asked questions 349.5 KB 2015/10/04

* We provide a default example in the ALICE software. Therefore, the file is somewhat large!

 

Download library files for Affymetrix Power Tools (APT):

Affymetrix Platform

100K 500K Array 6.0 Axiom (CHB 1)

File Size

19.6 MB 65.2 MB 79.8 MB 73.9MB
Original resource Hind, Xba Nsp, Sty Array6 Axiom CHB1

 

Download annotation files:

For Affymetrix:

Version

na28

(hg18/dbSNP 128)

na29
(hg18/dbSNP 128)

na30
(hg18/dbSNP 128)

na31
(hg19/dbSNP 131)

na32
(hg19/dbSNP 132)

na33
(hg19/dbSNP 137)

100K

na28 na29 na30 na31 na32  
500K na28 na29 na30 na31 na32  
Array 6.0 na28 na29 na30 na31 na32 na33
Axiom         na32 na33

 

For Illumina:

HumanHap550v3_B.csv

 

Download examples:

Example

1-1 1-2 1-3 2-1 2-2 2-3 3-1 3-2

Batch

        Batch Batch    
File size 390 MB 189 MB 189 MB 172 MB 147 MB 150 MB 219 MB 219 MB

 

Download database:

 

Han Chinese in Taiwan Asian CEU CHB JPT YRI Combined

 

 

 

 

 

 

 

Popultaion Platform Input data format Sample size

Parameter

(w, nc)

Database index (Description)
1 2 3 4 5 6 7 8

 

 

Han Chinese in Taiwan

 

Affymetrix

100K

GTC-exported

text file

367 (11 , 2) AFFY100K,TXT,w11,nc2,DB1 AFFY100K,TXT,w11,nc2,DB2 AFFY100K,TXT,w11,nc2,DB3 AFFY100K,TXT,w11,nc2,DB4 AFFY100K,TXT,w11,nc2,DB5 AFFY100K,TXT,w11,nc2,DB6 AFFY100K,TXT,w11,nc2,DB7 AFFY100K,TXT,w11,nc2,DB8
(51 , 3) AFFY100K,TXT,w51,nc3,DB1 AFFY100K,TXT,w51,nc3,DB2 AFFY100K,TXT,w51,nc3,DB3 AFFY100K,TXT,w51,nc3,DB4 AFFY100K,TXT,w51,nc3,DB5 AFFY100K,TXT,w51,nc3,DB6 AFFY100K,TXT,w51,nc3,DB7 AFFY100K,TXT,w51,nc3,DB8

Affymetrix

500K

GTC-exported

text file

448 (11 , 2) AFFY500K,TXT,w11,nc2,DB1 AFFY500K,TXT,w11,nc2,DB2 AFFY500K,TXT,w11,nc2,DB3 AFFY500K,TXT,w11,nc2,DB4 AFFY500K,TXT,w11,nc2,DB5 AFFY500K,TXT,w11,nc2,DB6 AFFY500K,TXT,w11,nc2,DB7 AFFY500K,TXT,w11,nc2,DB8
(51 , 3) AFFY500K,TXT,w51,nc3,DB1 AFFY500K,TXT,w51,nc3,DB2 AFFY500K,TXT,w51,nc3,DB3 AFFY500K,TXT,w51,nc3,DB4 AFFY500K,TXT,w51,nc3,DB5 AFFY500K,TXT,w51,nc3,DB6 AFFY500K,TXT,w51,nc3,DB7 AFFY500K,TXT,w51,nc3,DB8

Affymetrix

Array 6.0

Probe results

file (*.CEL)

1,013 (11 , 2) ARRAY6.0,CEL,w11,nc2,DB1 ARRAY6.0,CEL,w11,nc2,DB2 ARRAY6.0,CEL,w11,nc2,DB3 ARRAY6.0,CEL,w11,nc2,DB4 ARRAY6.0,CEL,w11,nc2,DB5 ARRAY6.0,CEL,w11,nc2,DB6 ARRAY6.0,CEL,w11,nc2,DB7 ARRAY6.0,CEL,w11,nc2,DB8
(51 , 3) ARRAY6.0,CEL,w51,nc3,DB1 ARRAY6.0,CEL,w51,nc3,DB2 ARRAY6.0,CEL,w51,nc3,DB3 ARRAY6.0,CEL,w51,nc3,DB4 ARRAY6.0,CEL,w51,nc3,DB5 ARRAY6.0,CEL,w51,nc3,DB6 ARRAY6.0,CEL,w51,nc3,DB7 ARRAY6.0,CEL,w51,nc3,DB8

GTC-exported

text file

1,013 (11 , 2) ARRAY6.0,TXT,w11,nc2,DB1 ARRAY6.0,TXT,w11,nc2,DB2 ARRAY6.0,TXT,w11,nc2,DB3 ARRAY6.0,TXT,w11,nc2,DB4 ARRAY6.0,TXT,w11,nc2,DB5 ARRAY6.0,TXT,w11,nc2,DB6 ARRAY6.0,TXT,w11,nc2,DB7 ARRAY6.0,TXT,w11,nc2,DB8
(51 , 3) ARRAY6.0,TXT,w51,nc3,DB1 ARRAY6.0,TXT,w51,nc3,DB2 ARRAY6.0,TXT,w51,nc3,DB3 ARRAY6.0,TXT,w51,nc3,DB4 ARRAY6.0,TXT,w51,nc3,DB5 ARRAY6.0,TXT,w51,nc3,DB6 ARRAY6.0,TXT,w51,nc3,DB7 ARRAY6.0,TXT,w51,nc3,DB8

Affymetrix

Axiom CHB

Probe results

file (*.CEL)

1,666 (11 , 2) AXIOM,CEL,w11,nc2,DB1 AXIOM,CEL,w11,nc2,DB2 AXIOM,CEL,w11,nc2,DB3 AXIOM,CEL,w11,nc2,DB4 AXIOM,CEL,w11,nc2,DB5 AXIOM,CEL,w11,nc2,DB6 AXIOM,CEL,w11,nc2,DB7 AXIOM,CEL,w11,nc2,DB8
(51 , 3) AXIOM,CEL,w51,nc3,DB1 AXIOM,CEL,w51,nc3,DB2 AXIOM,CEL,w51,nc3,DB3 AXIOM,CEL,w51,nc3,DB4 AXIOM,CEL,w51,nc3,DB5 AXIOM,CEL,w51,nc3,DB6 AXIOM,CEL,w51,nc3,DB7 AXIOM,CEL,w51,nc3,DB8

GTC-exported

text file

1,666 (11 , 2) AXIOM,TXT,w11,nc2,DB1 AXIOM,TXT,w11,nc2,DB2 AXIOM,TXT,w11,nc2,DB3 AXIOM,TXT,w11,nc2,DB4 AXIOM,TXT,w11,nc2,DB5 AXIOM,TXT,w11,nc2,DB6 AXIOM,TXT,w11,nc2,DB7 AXIOM,TXT,w11,nc2,DB8
(51 , 3) AXIOM,TXT,w51,nc3,DB1 AXIOM,TXT,w51,nc3,DB2 AXIOM,TXT,w51,nc3,DB3 AXIOM,TXT,w51,nc3,DB4 AXIOM,TXT,w51,nc3,DB5 AXIOM,TXT,w51,nc3,DB6 AXIOM,TXT,w51,nc3,DB7 AXIOM,TXT,w51,nc3,DB8
Illumina

BS-exported

text file

854 (11 , 2) ILMN,TXT,w11,nc2,DB1 ILMN,TXT,w11,nc2,DB2 ILMN,TXT,w11,nc2,DB3 ILMN,TXT,w11,nc2,DB4 ILMN,TXT,w11,nc2,DB5 ILMN,TXT,w11,nc2,DB6 ILMN,TXT,w11,nc2,DB7 ILMN,TXT,w11,nc2,DB8
(51 , 3) ILMN,TXT,w51,nc3,DB1 ILMN,TXT,w51,nc3,DB2 ILMN,TXT,w51,nc3,DB3 ILMN,TXT,w51,nc3,DB4 ILMN,TXT,w51,nc3,DB5 ILMN,TXT,w51,nc3,DB6 ILMN,TXT,w51,nc3,DB7 ILMN,TXT,w51,nc3,DB8

 

 

Popultaion Platform Input data format Sample size

Parameter

(w, nc)

Database index (Description)
1 2 3 4 5 6 7 8

 

Asian

(CHB + JPT)

 

Affymetrix

Array 6.0

Probe results

file (*.CEL)

90 (11 , 2) A6_HM_Asian90,CEL,w11,nc2,DB1 A6_HM_Asian90,CEL,w11,nc2,DB2 A6_HM_Asian90,CEL,w11,nc2,DB3 A6_HM_Asian90,CEL,w11,nc2,DB4 A6_HM_Asian90,CEL,w11,nc2,DB5 A6_HM_Asian90,CEL,w11,nc2,DB6 A6_HM_Asian90,CEL,w11,nc2,DB7 A6_HM_Asian90,CEL,w11,nc2,DB8
(51 , 3) A6_HM_Asian90,CEL,w51,nc3,DB1 A6_HM_Asian90,CEL,w51,nc3,DB2 A6_HM_Asian90,CEL,w51,nc3,DB3 A6_HM_Asian90,CEL,w51,nc3,DB4 A6_HM_Asian90,CEL,w51,nc3,DB5 A6_HM_Asian90,CEL,w51,nc3,DB6 A6_HM_Asian90,CEL,w51,nc3,DB7 A6_HM_Asian90,CEL,w51,nc3,DB8

 

 

Popultaion Platform Input data format Sample size

Parameter

(w, nc)

Database index (Description)
1 2 3 4 5 6 7 8

 

CEU

 

Affymetrix

Array 6.0

Probe results

file (*.CEL)

60 (11 , 2) A6_HM_CEU60,CEL,w11,nc2,DB1 A6_HM_CEU60,CEL,w11,nc2,DB2 A6_HM_CEU60,CEL,w11,nc2,DB3 A6_HM_CEU60,CEL,w11,nc2,DB4 A6_HM_CEU60,CEL,w11,nc2,DB5 A6_HM_CEU60,CEL,w11,nc2,DB6 A6_HM_CEU60,CEL,w11,nc2,DB7 A6_HM_CEU60,CEL,w11,nc2,DB8
(51 , 3) A6_HM_CEU60,CEL,w51,nc3,DB1 A6_HM_CEU60,CEL,w51,nc3,DB2 A6_HM_CEU60,CEL,w51,nc3,DB3 A6_HM_CEU60,CEL,w51,nc3,DB4 A6_HM_CEU60,CEL,w51,nc3,DB5 A6_HM_CEU60,CEL,w51,nc3,DB6 A6_HM_CEU60,CEL,w51,nc3,DB7 A6_HM_CEU60,CEL,w51,nc3,DB8

 

 

Popultaion Platform Input data format Sample size

Parameter

(w, nc)

Database index (Description)
1 2 3 4 5 6 7 8

 

CHB

 

Affymetrix

Array 6.0

Probe results

file (*.CEL)

45 (11 , 2) A6_HM_CHB45,CEL,w11,nc2,DB1 A6_HM_CHB45,CEL,w11,nc2,DB2 A6_HM_CHB45,CEL,w11,nc2,DB3 A6_HM_CHB45,CEL,w11,nc2,DB4 A6_HM_CHB45,CEL,w11,nc2,DB5 A6_HM_CHB45,CEL,w11,nc2,DB6 A6_HM_CHB45,CEL,w11,nc2,DB7 A6_HM_CHB45,CEL,w11,nc2,DB8
(51 , 3) A6_HM_CHB45,CEL,w51,nc3,DB1 A6_HM_CHB45,CEL,w51,nc3,DB2 A6_HM_CHB45,CEL,w51,nc3,DB3 A6_HM_CHB45,CEL,w51,nc3,DB4 A6_HM_CHB45,CEL,w51,nc3,DB5 A6_HM_CHB45,CEL,w51,nc3,DB6 A6_HM_CHB45,CEL,w51,nc3,DB7 A6_HM_CHB45,CEL,w51,nc3,DB8

 

 

Popultaion Platform Input data format Sample size

Parameter

(w, nc)

Database index (Description)
1 2 3 4 5 6 7 8

 

JPT

 

Affymetrix

Array 6.0

Probe results

file (*.CEL)

45 (11 , 2) A6_HM_JPT45,CEL,w11,nc2,DB1 A6_HM_JPT45,CEL,w11,nc2,DB2 A6_HM_JPT45,CEL,w11,nc2,DB3 A6_HM_JPT45,CEL,w11,nc2,DB4 A6_HM_JPT45,CEL,w11,nc2,DB5 A6_HM_JPT45,CEL,w11,nc2,DB6 A6_HM_JPT45,CEL,w11,nc2,DB7 A6_HM_JPT45,CEL,w11,nc2,DB8
(51 , 3) A6_HM_JPT45,CEL,w51,nc3,DB1 A6_HM_JPT45,CEL,w51,nc3,DB2 A6_HM_JPT45,CEL,w51,nc3,DB3 A6_HM_JPT45,CEL,w51,nc3,DB4 A6_HM_JPT45,CEL,w51,nc3,DB5 A6_HM_JPT45,CEL,w51,nc3,DB6 A6_HM_JPT45,CEL,w51,nc3,DB7 A6_HM_JPT45,CEL,w51,nc3,DB8

 

 

Popultaion Platform Input data format Sample size

Parameter

(w, nc)

Database index (Description)
1 2 3 4 5 6 7 8

 

YRI

 

Affymetrix

Array 6.0

Probe results

file (*.CEL)

60 (11 , 2) A6_HM_YRI60,CEL,w11,nc2,DB1 A6_HM_YRI60,CEL,w11,nc2,DB2 A6_HM_YRI60,CEL,w11,nc2,DB3 A6_HM_YRI60,CEL,w11,nc2,DB4 A6_HM_YRI60,CEL,w11,nc2,DB5 A6_HM_YRI60,CEL,w11,nc2,DB6 A6_HM_YRI60,CEL,w11,nc2,DB7 A6_HM_YRI60,CEL,w11,nc2,DB8
(51 , 3) A6_HM_YRI60,CEL,w51,nc3,DB1 A6_HM_YRI60,CEL,w51,nc3,DB2 A6_HM_YRI60,CEL,w51,nc3,DB3 A6_HM_YRI60,CEL,w51,nc3,DB4 A6_HM_YRI60,CEL,w51,nc3,DB5 A6_HM_YRI60,CEL,w51,nc3,DB6 A6_HM_YRI60,CEL,w51,nc3,DB7 A6_HM_YRI60,CEL,w51,nc3,DB8

 

 

Popultaion Platform Input data format Sample size

Parameter

(w, nc)

Database index (Description)
1 2 3 4 5 6 7 8

 

Combined

(CEU + CHB + JPT + YRI)

 

Affymetrix

Array 6.0

Probe results

file (*.CEL)

210 (11 , 2) A6_HM_Comb210,CEL,w11,nc2,DB1 A6_HM_Comb210,CEL,w11,nc2,DB2 A6_HM_Comb210,CEL,w11,nc2,DB3 A6_HM_Comb210,CEL,w11,nc2,DB4 A6_HM_Comb210,CEL,w11,nc2,DB5 A6_HM_Comb210,CEL,w11,nc2,DB6 A6_HM_Comb210,CEL,w11,nc2,DB7 A6_HM_Comb210,CEL,w11,nc2,DB8
(51 , 3) A6_HM_Comb210,CEL,w51,nc3,DB1 A6_HM_Comb210,CEL,w51,nc3,DB2 A6_HM_Comb210,CEL,w51,nc3,DB3 A6_HM_Comb210,CEL,w51,nc3,DB4 A6_HM_Comb210,CEL,w51,nc3,DB5 A6_HM_Comb210,CEL,w51,nc3,DB6 A6_HM_Comb210,CEL,w51,nc3,DB7 A6_HM_Comb210,CEL,w51,nc3,DB8