Initial Commit

.gitignore

+*~
+._*
\ No newline at end of file

LICENSE.txt

+MIT License
+
+Copyright (c) 2018: Elodie Laine, Yasaman Karami and Alessandra Carbone.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
\ No newline at end of file

README

+############################################################################################################
+#                                                                                                          #
+#    GEMME: a tool to predict mutational outcomes using evolutionary conservation and global epistasis     #
+#                                                                                                          #
+############################################################################################################
+#
+#
+# GEMME is implemented in Python and R.
+# https://www.python.org/
+# https://cran.r-project.org/
+#
+#
+##################
+# Dependencies:  #
+##################
+#
+#  Joint Evolutionary Trees: http://www.lcqb.upmc.fr/JET2/
+#  seqinr R package: https://cran.r-project.org/web/packages/seqinr/index.html
+#  These tools should be installed to be able to use GEMME.
+#
+#
+##################
+# Installation:  #
+##################
+#
+# Download the GEMME.tgz archive from http://www.lcqb.upmc.fr/GEMME/.
+# Uncompress the archive in the directory of your choice.
+# Define and export the environment variable GEMME_PATH=/path-to-GEMME-directory/
+# Run the program by typing "python $GEMME_PATH/gemme.py inputAli.fasta".
+# A help can be accessed by typing "python $GEMME_PATH/gemme.py --help".
+#
+#
+#################
+# Usage notes:  #
+#################
+# 
+# The inputAli.fasta is a mandatory argument that corresponds to the input multiple sequence 
+# alignment file, in FASTA format. The query sequence is taken as the first sequence in the alignment.
+#
+# By default, GEMME will predict the effect of all possible single mutations at all positions in the 
+# query sequence. Alternatively, a set of single or multiple mutations can be given with the option -m.
+# Eachline of the file should contain a mutation (e.g. D136R) or combination of mutations separated 
+# by commas and ordered according to their positions in the sequence (e.g. D136R,V271A).
+#
+# GEMME calls JET2 to compute evolutionary conservation levels. By default, JET2 will retrieve a set
+# of sequences related to the query, independent from the input set, according to specific criteria.
+# The retrieval method used in JET2 is PSI-BLAST, which can perform the search either locally (by 
+# default) or remotely (-r server). Alternatively, the user can provide her/his own psiblast file  
+# (-r input-b pFile) or her/his own multiple sequence alignment in FASTA format (-r input -f fFile).
+# JET is run in its iterative mode, iJET, 10 times and the final conservation levels are the maxium 
+# values obtained over the 10 iterations. 
+# JET2 configuration file is: default.conf.
+# JET2 output file is: myProt_jet.res.
+#
+# By default, GEMME will output mutational effects predictions obtained from the global epistatic model,
+# the independent model, and a combination of those two using a reduced alphabet (alphabets/lw-i.11.txt):
+# myProt_pred_evolEpi.txt
+# myProt_normPred_evolEpi.txt
+# myProt_pred_evolInd.txt
+# myProt_normPred_evolInd.txt
+# myProt_normPred_evolCombi.txt
+# The values of interest are the normalized predictions (normPred). Each file contains a 20 x n matrix, 
+# where n is the number of positions in the query sequence.
+# If the user provides her/his own list of mutations, then only the global epistatic model will be run 
+# and the output file will contain 2 columns, the first one with the mutations, the second one with the 
+# normalized predicted effects.
+#
+#
+####################
+# Main reference:  #
+####################
+#
+# Laine E, Karami Y, Carbone A. GEMME: A Simple and Fast Global Epistatic Model Predicting Mutational Effects
+# Molecular Biology and Evolution, Volume 36, Issue 11, November 2019, Pages 2604–2619
+#
+#
+#
+############################################################################################################
+

alphabets/ab.10.txt

+P
+G
+EKRQ
+DSN
+T
+HC
+IV
+WYF
+A
+LM

alphabets/ab.11.txt

+P
+G
+EKRQ
+D
+SN
+T
+HC
+IV
+WYF
+A
+LM

alphabets/ab.12.txt

+P
+G
+EKRQ
+D
+SN
+T
+H
+C
+IV
+WYF
+A
+LM

alphabets/ab.13.txt

+P
+G
+E
+KRQ
+D
+SN
+T
+H
+C
+IV
+WYF
+A
+LM

alphabets/ab.14.txt

+P
+G
+E
+KRQ
+D
+S
+N
+T
+H
+C
+IV
+WYF
+A
+LM

alphabets/ab.15.txt

+P
+G
+E
+KRQ
+D
+S
+N
+T
+H
+C
+IV
+W
+YF
+A
+LM

alphabets/ab.16.txt

+P
+G
+E
+KRQ
+D
+S
+N
+T
+H
+C
+IV
+W
+YF
+A
+L
+M

alphabets/ab.17.txt

+P
+G
+E
+K
+RQ
+D
+S
+N
+T
+H
+C
+IV
+W
+YF
+A
+L
+M

alphabets/ab.18.txt

+P
+G
+E
+K
+RQ
+D
+S
+N
+T
+H
+C
+I
+V
+W
+YF
+A
+L
+M

alphabets/ab.19.txt

+P
+G
+E
+K
+R
+Q
+D
+S
+N
+T
+H
+C
+I
+V
+W
+YF
+A
+L
+M

alphabets/ab.2.txt

+PGEKRQDSNTHC
+IVWYFALM

alphabets/ab.3.txt

+PG
+EKRQDSNTHC
+IVWYFALM

alphabets/ab.4.txt

+PG
+EKRQDSNTHC
+IVWYF
+ALM

alphabets/ab.5.txt

+PG
+EKRQ
+DSNTHC
+IVWYF
+ALM

alphabets/ab.6.txt

+PG
+EKRQ
+DSN
+THC
+IVWYF
+ALM

alphabets/ab.7.txt

+PG
+EKRQ
+DSN
+THC
+IVWYF
+A
+LM

alphabets/ab.8.txt

+P
+G
+EKRQ
+DSN
+THC
+IVWYF
+A
+LM

alphabets/ab.9.txt

+P
+G
+EKRQ
+DSN
+THC
+IV
+WYF
+A
+LM

alphabets/cb.2.txt

+LFIMVWCY
+HATGPRQSNEDK

alphabets/cb.5.txt

+LFI
+MVWCY
+HA
+TGPRQSNED
+K

alphabets/dssp.10.txt

+EKQR
+IV
+LY
+F
+AM
+W
+HT
+C
+DNS
+GP

alphabets/dssp.11.txt

+AEKQR
+IV
+LM
+F
+Y
+W
+C
+H
+T
+DNS
+GP

alphabets/dssp.12.txt

+AEKQR
+I
+V
+LM
+F
+Y
+W
+C
+H
+T
+DNS
+GP

alphabets/dssp.13.txt

+AEKQR
+I
+V
+L
+M
+F
+Y
+W
+C
+H
+T
+DNS
+GP

alphabets/dssp.14.txt

+DEKQ
+R
+A
+I
+V
+L
+M
+F
+Y
+W
+C
+H
+T
+GNPS

alphabets/dssp.2.txt

+ACEFHIKLMQRVWY
+DGNPST
\ No newline at end of file

alphabets/dssp.3.txt

+AEHKQR
+CFILMVWY
+DGNPST
\ No newline at end of file

alphabets/dssp.4.txt

+AEHKQR
+CFILMVWY
+DNST
+GP
\ No newline at end of file

alphabets/dssp.5.txt

+AEHKQR
+FILMVWY
+CST
+DN
+GP
\ No newline at end of file

alphabets/dssp.6.txt

+AEKQR
+FIV
+LMWY
+HCT
+DNS
+GP

alphabets/dssp.7.txt

+EKQR
+FIV
+LMWY
+ACH
+ST
+DN
+GP

alphabets/dssp.8.txt

+EKQR
+IV
+LWY
+AM
+CF
+HT
+DNS
+GP

alphabets/dssp.9.txt

+EKQR
+IV
+L
+F
+AMW
+CY
+HT
+DNS
+GP

alphabets/gbmr.10.txt

+G
+D
+N
+AEFIKLMQRVW
+Y
+H
+C
+T
+S
+P
\ No newline at end of file

alphabets/gbmr.11.txt

+G
+D
+N
+AEFIKLMQRV
+W
+Y
+H
+C
+T
+S
+P
\ No newline at end of file

alphabets/gbmr.12.txt

+G
+D
+N
+AEFIKLMQV
+R
+W
+Y
+H
+C
+T
+S
+P
\ No newline at end of file

alphabets/gbmr.13.txt

+G
+D
+N
+AEFIKLMV
+Q
+R
+W
+Y
+H
+C
+T
+S
+P
\ No newline at end of file

alphabets/gbmr.14.txt

+G
+D
+N
+AEFIKLV
+M
+Q
+R
+W
+Y
+H
+C
+T
+S
+P
\ No newline at end of file

alphabets/gbmr.2.txt

+GP
+DNAEFIKLVMQRWYHCTS

alphabets/gbmr.3.txt

+G
+DNAEFIKLVMQRWYHCTS
+P

alphabets/gbmr.4.txt

+G
+ADEKNQRST
+CFHILMVWY
+P

alphabets/gbmr.5.txt

+G
+ND
+AEHKQRST
+CFILMVWY
+P
\ No newline at end of file

alphabets/gbmr.6.txt

+G
+DN
+AEFHIKLMQRVWY
+CT
+S
+P
\ No newline at end of file

alphabets/gbmr.7.txt

+G
+DN
+AEFIKLMQRVWY
+CH
+T
+S
+P
\ No newline at end of file

alphabets/gbmr.8.txt

+G
+D
+N
+AEFIKLMQRVWY
+CH
+T
+S
+P
\ No newline at end of file

alphabets/gbmr.9.txt

+G
+D
+N
+AEFIKLMQRVWY
+H
+C
+T
+S
+P
\ No newline at end of file

alphabets/grud7.txt

+FWYM
+CLIV
+AP
+NST
+GH
+DE
+KQR

alphabets/grud9.txt

+FWYM
+H
+LIVC
+A
+NST
+P
+G
+DE
+KQR

alphabets/hsdm.10.txt

+LIVFM
+Y
+W
+C
+DN
+TSKEQR
+A
+G
+P
+H
\ No newline at end of file

alphabets/hsdm.12.txt

+LIVF
+M
+Y
+W
+C
+DN
+TSKEQ
+R
+A
+G
+P
+H
\ No newline at end of file

alphabets/hsdm.14.txt

+LIV
+F
+M
+Y
+W
+C
+DN
+TS
+KEQ
+R
+A
+G
+P
+H
\ No newline at end of file

alphabets/hsdm.15.txt

+LIV
+F
+M
+Y
+W
+C
+D
+N
+TS
+KEQ
+R
+A
+G
+P
+H
\ No newline at end of file

alphabets/hsdm.16.txt

+LIV
+F
+M
+Y
+W
+C
+D
+N
+TS
+KE
+Q
+R
+A
+G
+P
+H
\ No newline at end of file

alphabets/hsdm.17.txt

+LIV
+F
+M
+Y
+W
+C
+D
+N
+T
+S
+KE
+Q
+R
+A
+G
+P
+H
\ No newline at end of file

alphabets/hsdm.2.txt

+LIVFMYWC
+DNTSKEQRAGPH
\ No newline at end of file

alphabets/hsdm.3.txt

+LIVFMYW
+C
+DNTSKEQRAGPH
\ No newline at end of file

alphabets/hsdm.4.txt

+LIVFMYW
+C
+DNTSKEQRAGP
+H
\ No newline at end of file

alphabets/hsdm.5.txt

+LIVFMY
+W
+C
+DNTSKEQRAGP
+H
\ No newline at end of file

alphabets/hsdm.6.txt

+LIVFMY
+W
+C
+DNTSKEQRAG
+P
+H
\ No newline at end of file

alphabets/hsdm.7.txt

+LIVFMY
+W
+C
+DNTSKEQRA
+G
+P
+H
\ No newline at end of file

alphabets/hsdm.8.txt

+LIVFM
+Y
+W
+C
+DNTSKEQRA
+G
+P
+H
\ No newline at end of file

alphabets/hsdm.9.txt

+LIVFM
+Y
+W
+C
+DNTSKEQR
+A
+G
+P
+H
\ No newline at end of file

alphabets/lr.10.txt

+AST
+C
+DEN
+FY
+G
+H
+ILMV
+KQR
+P
+W

alphabets/lw-i.10.txt

+FWY
+ML
+IV
+CA
+TS
+NH
+P
+G
+DE
+QRK

alphabets/lw-i.11.txt

+FWY
+ML
+IV
+CA
+TS
+NH
+P
+G
+D
+QE
+RK

alphabets/lw-i.12.txt

+FWY
+ML
+IV
+C
+A
+TS
+NH
+P
+G
+D
+QE
+RK

alphabets/lw-i.13.txt

+FWY
+ML
+IV
+C
+A
+T
+S
+NH
+P
+G
+D
+QE
+RK

alphabets/lw-i.14.txt

+FWY
+ML
+IV
+C
+A
+T
+S
+NH
+P
+G
+D
+QE
+R
+K

alphabets/lw-i.15.txt

+FWY
+ML
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+QE
+R
+K

alphabets/lw-i.16.txt

+W
+FY
+ML
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+QE
+R
+K

alphabets/lw-i.17.txt

+W
+FY
+ML
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+Q
+E
+R
+K

alphabets/lw-i.18.txt

+W
+FY
+M
+L
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+Q
+E
+R
+K

alphabets/lw-i.19.txt

+W
+F
+Y
+M
+L
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+Q
+E
+R
+K

alphabets/lw-i.2.txt

+CMFILVWY
+AGTSNQDEHRKP

alphabets/lw-i.3.txt

+CMFILVWY
+AGTSP
+NQDEHRK

alphabets/lw-i.4.txt

+CMFWY
+ILV
+AGTS
+NQDEHRKP

alphabets/lw-i.5.txt

+FWYH
+MILV
+CATSP
+G
+NQDERK

alphabets/lw-i.6.txt

+FWYH
+MILV
+CATS
+P
+G
+NQDERK

alphabets/lw-i.7.txt

+FWYH
+MILV
+CATS
+P
+G
+NQDE
+RK

alphabets/lw-i.8.txt

+FWYH
+MILV
+CA
+NTS
+P
+G
+DE
+QRK

alphabets/lw-i.9.txt

+FWYH
+ML
+IV
+CA
+NTS
+P
+G
+DE
+QRK

alphabets/lw-ni.10.txt

+C
+FYW
+ML
+IV
+G
+P
+ATS
+NH
+QED
+RK

alphabets/lw-ni.11.txt

+C
+FYW
+ML
+IV
+G
+P
+A
+TS
+NH
+QED
+RK

alphabets/lw-ni.12.txt

+C
+FYW
+ML
+IV
+G
+P
+A
+TS
+NH
+QE
+D
+RK

alphabets/lw-ni.13.txt

+C
+FYW
+ML
+IV
+G
+P
+A
+T
+S
+NH
+QE
+D
+RK

alphabets/lw-ni.14.txt

+C
+FYW
+ML
+IV
+G
+P
+A
+T
+S
+N
+H
+QE
+D
+RK

alphabets/lw-ni.15.txt

+FWY
+ML
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+QE
+R
+K

alphabets/lw-ni.16.txt

+W
+FY
+ML
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+QE
+R
+K

alphabets/lw-ni.17.txt

+W
+FY
+ML
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+Q
+E
+R
+K

alphabets/lw-ni.18.txt

+W
+FY
+M
+L
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+Q
+E
+R
+K

alphabets/lw-ni.19.txt

+W
+F
+Y
+M
+L
+IV
+C
+A
+T
+S
+N
+H
+P
+G
+D
+Q
+E
+R
+K

alphabets/lw-ni.2.txt

+CFYWMLIV
+GPATSNHQEDRK

alphabets/lw-ni.3.txt

+CFYWMLIV
+GPATS
+NHQEDRK

alphabets/lw-ni.4.txt

+CFYW
+MLIV
+GPATS
+NHQEDRK

alphabets/lw-ni.5.txt

+CFYW
+MLIV
+G
+PATS
+NHQEDRK

alphabets/lw-ni.6.txt

+CFYW
+MLIV
+G
+P
+ATS
+NHQEDRK

alphabets/lw-ni.7.txt

+CFYW
+MLIV
+G
+P
+ATS
+NHQED
+RK