Download prebuild static executables for Windows, Linux and Mac.
Warning. The installer and the program doesn't work from a directory with non-ascii letters in name.
BLAST and other dependencies (except Qt 4
in Linux version) are included. Warning. To use
Linux version, you should install Qt4 library.
In Debian or Ubuntu Qt4 can be installed by command
sudo apt-get install libqtgui4.
In the following instructions, replace
the version of NPG-explorer you use.
For Windows 32 bit, download and run file
npge_x.y.z_win32.exe as administrator.
For Windows 64 bit, download and run file
npge_x.y.z_win64.exe as administrator.
For Linux 64 bit, download and unpack file
tar -xf npge_x.y.z_lin64.tar.gz).
Windows version adds itself to PATH, so you can use
qnpge in command line.
In Linux, you need to add the unpacked directory
npge-x.y.z to PATH. If you use
~/.bashrc in your favorite text editor
and add the following line to the end:
Do not forget to replace
with the actual path.
Create a directory for the results
All files with data and output files have fixed names. This is why it is recomended to make separate working directory for each task.
Prepare files with genomes
Input file: table of genomes
genomes.tsv of the form:
all:embl:CP003176 BRUAO chr1 c Brucella abortus A13334 chr 1 all:embl:CP003177 BRUAO chr2 c Brucella abortus A13334 chr 2 fasta:refseqn:NC_016778.1 BRUCA chr1 c Brucella canis HSK A52141 chr 1 features:embl:CP003174 BRUCA chr1 c Brucella canis HSK A52141 chr 1 fasta:file:BRUCA.fasta BRUCA chr1 c Brucella canis HSK A52141 chr 1 features:file:BRUCA.fasta BRUCA chr1 c Brucella canis HSK A52141 chr 1 fasta:file:base.fasta[CP002459] BRUMM chr1 c Brucella melitensis features:file:base.embl[CP002459] BRUMM chr1 c Brucella melitensis
- chromosome entry identifier; it is composed from
record type ('fasta', 'features' (annotation) or 'all'),
source (database name or 'file')
and identifier in that database or file path;
it is possible to get annotations and fasta files
from different sources;
file.fasta[name_of_sequence]as an identifier to copy specific sequence from file;
- short name for the genome chosen by user,
this name is used in output data;
this name must not include spaces or underscores
(more precisely, it must not look like a fragment
- chromosome name (e.g., 'chr1', 'chr2'),
- chromosome circularity ('c' for circular and 'l' for linear), and arbitrary description (not used by the program).
The program downloads input data using dbfetch.
Annotations in the following formats are parsed by the program: GenBank, EMBL.
CP003175 BRUCA chr2 c corresponds to EMBL entry
CP003175 which is represented by short genome name
BRUCA, chromosome name
chr2 and is circular.
You can use contigs instead of chromosomes, if genome is not fully assembled. Set circularity to 'l' in this case.
Create empty directory and create file
with the table of genomes to be used to build pangenome.
npge will create files and sub-folders
in current directory.
You can change location of output files using command
line options. To see all options, add
-h to a command.
To set path to table file (instead of
--table to commands
GetFasta, GetGenes and Rename.
Examples of genomes.tsv
Examples of genomes.tsv files can be found in directory examples of the source code.
Here we provide a table for 3 Brucella genomes:
all:embl:CP002459 BRUMM chr1 c Brucella melitensis M28 chromosome 1 all:embl:CP002460 BRUMM chr2 c Brucella melitensis M28 chromosome 2 all:embl:CP003176 BRUAO chr1 c Brucella abortus A13334 chromosome 1 all:embl:CP003177 BRUAO chr2 c Brucella abortus A13334 chromosome 2 all:embl:CP002078 BRUPB chr1 c Brucella pinnipedialis B2/94 chromosome 1 all:embl:CP002079 BRUPB chr2 c Brucella pinnipedialis B2/94 chromosome 2
... and for 17 Brucella genomes as well:
all:embl:CP003176 BRUAO chr1 c Brucella abortus A13334 chromosome 1 all:embl:CP003177 BRUAO chr2 c Brucella abortus A13334 chromosome 2 all:embl:CP003174 BRUCA chr1 c Brucella canis HSK A52141 chromosome 1 all:embl:CP003175 BRUCA chr2 c Brucella canis HSK A52141 chromosome 2 all:embl:CP002459 BRUMM chr1 c Brucella melitensis M28 chromosome 1 all:embl:CP002460 BRUMM chr2 c Brucella melitensis M28 chromosome 2 all:embl:CP001851 BRUM5 chr1 c Brucella melitensis M5-90 chromosome I all:embl:CP001852 BRUM5 chr2 c Brucella melitensis M5-90 chromosome II all:embl:CP002931 BRUML chr1 c Brucella melitensis NI chromosome I all:embl:CP002932 BRUML chr2 c Brucella melitensis NI chromosome II all:embl:CP002078 BRUPB chr1 c Brucella pinnipedialis B2/94 chromosome 1 all:embl:CP002079 BRUPB chr2 c Brucella pinnipedialis B2/94 chromosome 2 all:embl:CP003128 BRUSS chr1 c Brucella suis VBI22 chromosome I all:embl:CP003129 BRUSS chr2 c Brucella suis VBI22 chromosome II all:embl:AE017223 BRUAB chr1 c Brucella abortus biovar 1 str. 9-941 chromosome I all:embl:AE017224 BRUAB chr2 c Brucella abortus biovar 1 str. 9-941 chromosome II all:embl:CP000887 BRUA1 chr1 c Brucella abortus S19 chromosome 1 all:embl:CP000888 BRUA1 chr2 c Brucella abortus S19 chromosome 2 all:embl:AM040264 BRUA2 chr1 c Brucella melitensis biovar Abortus 2308 chromosome I all:embl:AM040265 BRUA2 chr2 c Brucella melitensis biovar Abortus 2308 chromosome II all:embl:CP000872 BRUC2 chr1 c Brucella canis ATCC 23365 chromosome I all:embl:CP000873 BRUC2 chr2 c Brucella canis ATCC 23365 chromosome II all:embl:CP001488 BRUMB chr1 c Brucella melitensis ATCC 23457 chromosome I all:embl:CP001489 BRUMB chr2 c Brucella melitensis ATCC 23457 chromosome II all:embl:AE008917 BRUME chr1 c Brucella melitensis bv. 1 str. 16M chromosome I all:embl:AE008918 BRUME chr2 c Brucella melitensis 16M chromosome II all:embl:CP001578 BRUMC chr1 c Brucella microti CCM 4915 chromosome 1 all:embl:CP001579 BRUMC chr2 c Brucella microti CCM 4915 chromosome 2 all:embl:CP000708 BRUO2 chr1 c Brucella ovis ATCC 25840 chromosome I all:embl:CP000709 BRUO2 chr2 c Brucella ovis ATCC 25840 chromosome II all:embl:AE014291 BRUSU chr1 c Brucella suis 1330 chromosome I all:embl:AE014292 BRUSU chr2 c Brucella suis 1330 chromosome II all:embl:CP000911 BRUSI chr1 c Brucella suis ATCC 23445 chromosome I all:embl:CP000912 BRUSI chr2 c Brucella suis ATCC 23445 chromosome II
The latter one is used below.
Open the command line
Further steps are performed in the command line.
Linux users are expected to be familiar with the command line.
How to launch the command line in Windows:
- press Win+R on your keyboard to open it;
cmdand press Enter;
cd path/to/directory+ Enter to navigate to the directory with file
- to switch to other disk, type its label followed by
:+ Enter, for example
D:+ Enter to switch to disk
- type the commands from the following sections without
$, for example,
npge Prepare+ Enter.
Prepare sequences and genes
Run the following command:
$ npge Prepare
The following files are created by this command:
genomes-renamed.fastais FASTA file with genomes on with a nucleotide pangenome is to be built;
genes/features.bsis a blockset of genes. One gene is represented as one block.
unprocessed input data.
They are not used by following steps.
You can safely remove them.
Examine prepared sequences
Run the following command:
$ npge Examine
The following files are created by this command in
genomes-info.tsvtable of genome lengths; make sure genome lengths are about the same, otherwise do not expect NPG-explorer to build good pangenome;
identity_recommended.txttext file with recommended value of parameter
MIN_IDENTITY(see below how to change this parameter in configuration file).
This step is needed to gather some information about input genomes. This information can be used on next step (configuration).
Set values of global options
To change values of global options, make file
npge -g npge.conf, then edit this file
to change values of global options.
npge.conf contains default values compiled into
the program. Sometimes they have to be changed to
Configuration file looks like this:
MIN_IDENTITY = Decimal('0.9') MIN_LENGTH = 100
Decimal values are specified using the syntax above. Accuracy of decimal values is 4 digits after the point.
The program applies following configuration files (if exist):
npge.confin current directory;
npge.confin the program's directory (directory where the executable lives);
- reads environmental variables named like known options;
npge.confin current directory (again);
- applies command line options if passed.
Build nucleotide pangenome
$ npge MakePangenome
This command creates file
The file is in BlockSet format.
Check nucleotide pangenome (optional)
$ npge CheckPangenome
This command makes sure that nucleotide pangenome
The command prints if the pangenome is Ok and may print some comments about the pangenome.
This step is done by post-processing as well,
result is saved to file
Run post-processing of nucleotide pangenome
$ npge PostProcessing
This command produces many files, some of them are located in sub-folders.
*.bs contain blocksets,
*.bi contain tables of blocks' properties,
*.ba contain blockset alignments (cells are fragments)
*.blocks contain blockset alignments (cells are blocks)
Columns of files
- name of the block;
- number of fragments in the block;
- length of the alignment of the block;
- number of identical columns with no gaps;
- number of identical columns with gaps;
- number of nonidentical columns with no gaps;
- number of nonidentical columns with gaps;
- number of columns containing only gaps (must be 0);
- identity (from 0.0 to 1.0);
- percentage of 'G' and 'C' nucleotides in the block (from 0.0 to 1.0).
*.bi also contain numbers of occurrences of a block
in a genome. Each genome adds one column to the table.
To add similar columns with numbers of occurrences of
a block in a sequence, add option
pangenome/pangenome-small.bi contains short version of
pangenome/pangenome.bi, that lacks columns with occurrences
Files produced by
npge MakePangenome and
are as follows:
pangenome/pangenome.bspangenome (main output of the program);
pangenome/fragments.tsvtable with coordinates of all fragments in form: block, genome, chromosome, ac, start, stop, ori;
pangenome/pangenome.bablockset alignment. Table file representing alignment in which "letters" are fragments of pangenome. This file is used by GUI viewer
pangenome/pangenome.blocksblockset alignment. Table file representing alignment in which "letters" are blocks names. This file can be viewed in Excell. It is not used by
global-blocks/blocks.bsglobal blocks (blockset). Global blocks are joined collinear s-blocks;
global-blocks/blocks.baglobal blocks (blockset alignment of fragments). This file is used by GUI viewer
global-blocks/blocks.blocksglobal blocks (blockset alignment of blocks).
global-blocks/blocks.gbiproperties of global blocks as a table;
global-blocks/global-fragments.tsvproperties of fragments of global blocks as a table;
pangenome/pangenome.hashhash of pangenome;
pangenome/pangenome.infosummary of pangenome stats (average identity of blocks, etc);
extra-blocks/split.biblocks, splitted by diagnostic positions. This file is used by GUI viewer
extra-blocks/low.biSubblocks of low identity sliced from pangenome blocks. See explanation for more information about low identity subblocks. This file is used by GUI viewer
checkfiles related to pangenome checking;
isgoodresult of check that the pangenome pangenome criteria;
hits.blastoutput of BLAST all-against-all run on consensuses;
filtered-hits.blastfiltered output of BLAST all-against-all run on consensuses (self-hits, reverse hits, short hits and hits of low identity were removed);
all-blast-hits.biall BLAST hits as blocksets;
good-blast-hits.biBLAST hits satisfying pangenome criteria, which surpass overlapping blocks from the pangenome. If pangenome satisfies the criteria, there are no such blocks;
non-internal-hits.biBLAST hits satisfying pangenome criteria, which don't surpass overlapping blocks from the pangenome;
joined.bijoined subsequent blocks satisfying the criteria;
mutationsmutations related files:
mut.tsvtable of all mutations (columns are block, fragment, start of mutation, stop of mutation, letter(s) in consensus, letter (or gap) in the fragment); See file
src/tool/parse-mutations-file.pyfor example of how to parse file
mutseq.fastaFASTA file with sequences composed of columns with mutations (+ 1 columns to right and to left) of stable blocks;
mutseq-with-blocks.bssame as previous + stable blocks mapped of these sequences;
consensuses.fastaconsensus sequences of blocks;
genesanalysis of genes:
genes/partition-ungrouped.tsvmap of genes onto blocks;
genes/partition-grouped.tsvmap of genes onto blocks, grouped by gene fragment;
genes/good.bsgroups of genes matching each other exactly accourding to s-blocks;
genes/good-upstreams.bsupstream sequences of good genes (
treestree related files:
nj-global-tree.treglobal tree constructed using Neighbour-Joining applied to genome distances;
How to view
.trefiles using FigTree: open a file with FigTree, set branch label to "Diagnostic positions" in pop-up window, go to "Branch Labels" section of left menu, enable the section's checkbox. Abstract distances between nodes are shown under branches. To show number of diagnostic positions between corresponding clades, select "Diagnostic positions" in drop-down list.
View results in graphical user interface
This command uses
pangenome/pangenome.bs and some of files
created by PostProcessing.
The program window is splitted to 3 parts:
- top left is the table of genomes;
- top right is the blockset alignment (may be absent
if there is no file
- bottom is alignment of selected block.
Columns of blocks table:
- number of fragments in a block;
- length of a block;
- identity of a block;
- percentage of 'G' and 'C' nucleotides in the block;
- number of genes overlapping with a block;
- number of parts splitted from a block;
- number of low similarity regions.
You can filter blocks by block name, gene name or their
sequence using input located up to block table.
By default, pattern matching is wildcard.
^ before the pattern and
$ after the pattern
correspond to name start/end (as in regular expressions).
To hide blocks of one fragment, clock checkbox
"only blocks of >= 2 fragments".
Blocks table can be sorted by any column.
Blockset alignment table shows alignment of fragment on genomes. Chromosome can be selected using drop-down list located up to blockset table. Each sequence is represented as a row of blockset table. Name of a sequence and its orientation against the alignment is written in first column. Fragments of a sequence are represented by cells of blockset table. Fragments of one block are coloured similarly. Orientation of a fragment against the alignment is indicated by '<' and '>'.
When you navigate in blocks table and blockset alignment, the alignment of the corresponding block is shown in bottom part of the program. Fragment name is shown left to alignment itself. Background colors in alignment correspond to nucleotide types. Name of the selected gene is shown in read-only input located up to the alignment. You can disable genes representation completely by unchecking the checkbox "show genes". Genes are coloured with foreground color white. Genes on reverse chain (relatively to the fragment orientation) are marked with underscore. Overlapping genes are coloured with purple. Start codons are coloured with black, stop codons are coloured with gray. Consensus of the block is shown up to the alignment. Identical columns without gaps are coloured with black, identical columns with gaps are coloured with gray, non-identical columns are white. Columns numbers are shown up to consensus.
Columns numbers of low similarity regions are coloured with red. Low similarity regions represent parts of blocks with unreliable alignment. There are 3 possible reasons of occurrence of low similarity blocks:
- these sequences are not related,
- deletion and insertion in the same position.
You can use arrows keys to navigate through the alignment.
Corresponding fragment is selected in blockset alignment.
Use keys "Home" and "End" to go to first and last columns
of the alignment respectively.
If you "go away" from the alignment, the program
switches to corresponding block.
You go to next gene boundary if you press
Ctrl + Arrow Right
Ctrl + Arrow Left.
You go to next low similarity region
if you press
Shift + Arrow Right
Shift + Arrow Left.
To change order of sequences in blockset alignment
and block alignment, select some rows (you can use
select multiple rows) and press
Ctrl + Arrow Up
Ctrl + Arrow Down.
Requirements of a good pangenome
- no overlapping blocks;
- sequences are covered entirely by blocks (including 1-fragment blocks);
- alignment is defined for each block of >= 2 fragments;
- length of any block except minor blocks
is greater or equal to
- identity of any subsequent
FRAME_LENGTHcolumns of any but minor block is greater or equal to
- first and last columns of blocks do not contain gaps or dangling letters (few letters followed by long gaps);
- identity of
MIN_ENDfirst and last columns of any but minor block is greater or equal to
- blast run on consensuses finds no blocks which satisfy above criteria and surpass overlapping blocks from pangenome;
- no subsequent blocks can be joined so that resulting block satisfies above criteria.
Major blocks = non-minor blocks.
Build and Install
Main executables are command line tool src/tool/npge (or src/tool/npge.exe) and GUI tool src/gui/qnpge (src/gui/qnpge.exe).
To change compiled-in default settings,
ccmake . in build directory.
To generate config file, run
npge -g npge.conf and
change generated file
- C++ compiler (C++11 is not needed);
- Build system: make, cmake;
- Boost library (tested with version 1.42);
- Lua (version 5.1 or 5.2) or LuaJIT;
- LuaBind library;
- ZLIB library;
- BLAST legacy or BLAST plus (run-time requirement).
Warning. Make sure you use the same Lua which luabind was linked against. Otherwise it compiles but doesn't work:
PANIC: unprotected error in call to Lua API (attempt to index a nil value)
- Qt library (tested with version 4.8) for GUI;
- Readline and NCurses libraries for advanced Lua terminal;
- Doxygen to build documentation;
- Markdown builder (e.g. Pandoc) to make README.html;
- a viewer for trees in Newick format (FigTree, MEGA), to view phylogenetic trees of genomes.
To build static Linux package in fresh Debian Wheezy, install curl and sudo and run
curl -L https://git.io/vmB9P | sh
Install build requirements (on Debian):
Build the program as static executables (Qt 4 is not static!):
The program is built in the directory
npge-build-linux and run:
How to build manually:
$ ./src/init_lua-npge.sh $ mkdir build $ cd build $ cmake .. $ make
-DNPGE_STATIC_LINUX:BOOL=1 to after
to get static executables (on Debian, Qt 4 is not static!).
$ pandoc -s -o README.html README.md
$ make test
To build static Windows packages in fresh Debian Wheezy, install curl and sudo and run
curl -L https://git.io/vmB9v | sh
Windows executables are cross-compiled from Linux using MinGW cross-compiler.
For 64-bit Windows you need to export
$ export MXE_TARGET=x86_64-w64-mingw32.static
Install build requirements (on Debian):
Build the program as static executables:
The program is built in the directories
(first contains 32-bit version and
second contains 64-bit version).
Create ZIP file and Installation Wizard for Windows,
go into build directory (
npge-build-windows64) and run:
Version 0.5.8. Bug fix.
- AddGenes: fix bug with shift of genes names
Version 0.5.7. Bug fix.
- Info: don't print info about identity of g-blocks.
Version 0.5.6. Bug fixes and improvements.
- Bug fixes:
- GUI: fix detection of CDS for start/stop codones.
- Log: fix error when printing sizes in Lua 5.3.
- Fix possible crash in GUI.
- New PostProcessing outputs:
npge SampleGenomesTsvgenerates genomes.tsv.
- Documentation: greedy multiple alignment.
- Improve output of npge --help.
- Without options: prints help and exit.
- Wizard: remove useless menu items.
- AddGenes: produce a warning if no genes were found.
- README: add a section about openning command line.
- Move some configuration options to other sections.
- Bug fixes:
Version 0.5.5. Improvements.
- Improve logs produced by Prepare and MakePangenome.
- New output: pangenome/fragments.tsv.
- Embed lua-npge.
- MakePangenome: stop iterations if changes are small.
- Parse fragment IDs produced by lua-npge.
- GUI: prevent qnpge from printing -1 for fragment end.
- Pass info about AC to PostProcessing.
- Windows: add icon to .exe files.
- Doc: add texts about compare-pangenomes.
- Several improvements and bugfixes of build and deploy.
Version 0.5.4. Compatibility with Debian Squeeze. Starting with this version, Linux tarballs are built in Debian Squeeze machine to produce a binary compatible with wide range of Linux distributions.
Version 0.5.3. Bug fixes.
- GUI: fixes for overlapping genes
- PrintPartition: clusterisation and alignment of gene parts
- Info: produce info about g-blocks
- Info, Stats: print results as a table
- several improvements of build and distribution
Version 0.5.2. Bug fixes.
- Fix Windows build
- Workaround for gcc5 bug
- Disable LuaJIT explicitly
- algo_lua.cpp: Lua 5.3 compatibility
- fix windows build warning
- Fix typos and errors in README and Info's output
- config: do not fail with lua-npge npge.conf
- Fix Windows build
Version 0.5.1. Bug fixes and few improvements.
- Pangenome: join collinear blocks even if bad.
- Fix intermediate fragments joining. This bug was introduced in 2c76b512a3eaffc613cf5422c94394f37d24f297 (2015-05-16), version 0.4.0 (2015-06-12).
- Update requirements of a good pangenome in README.md according to what is implemented now.
- Genes-vs-blocks partition: print only
- GUI: jump to fragment end if there is no gene end.
- Info: print % of NPG for total blocks length.
- Recognize lua-npge format of Fragment id encoding.
- Download compressed files from the database.
- Fix errors in GetData and AddGenes.
- AddGenes: skip repeated
- Fix some build issues on various setups.
meta_test: ignore directories without script.npge.
- Setup Travis for cross-compiling to Windows (MXE).
- Setup Travis for uploading build artifacts to GitHub.
- Update BLAST in the distribution to 2.2.31.
Version 0.5.0. Bug fixes and few improvements.
- Change alignment requirements.
- Change meaning and default value of
- Add option
- Change meaning and default value of
- Add processor CountSMS
- Filter: increase size of gap score table to 1000
- BLAST version: 2.2.29 -> 2.2.30
- Option npge -v [--version]
- Clarify option -g
- Hide option
- GUI: show % of length occupied by low similarity
- Examine: do not recommend nan identity
- ECCB'14: add abstract in English (original)
- README: meaning of columns of *.bi files
- README: add blocks types algorithm (image)
- Fix bugs.
- FreeBSD build fixes. Thanks to Dmitry Marakasov!
- Fix segfault in PrintPartition.
- Fix the bug in BlastFinder (crash on empty input).
- Fix windows x64 build.
- Do not apply UPX to 64-bit Windows executables.
- Lua code: compatibility with Lua >= 5.2.
- Find more locus_tag's in GeneBank files.
- FindLowSimilar: fix division by zero.
- Change alignment requirements.
Version 0.4.0. Improvements.
- Change alignment requirements. Require high similarity in
every slice of length
MIN_LENGTH. Use logarithmic gap penalty. Introduce option
MIN_END. Do not require length of fragment >=
- Short blocks of one fragment are now called minor blocks.
All minor blocks are shorter than
- GUI/BSA: show block's length for global blocks.
- Use Travis CI: https://travis-ci.org/npge/npge
- BlockSet alignment: g-blocks and i-blocks. G-blocks are formed from joined consequent s-blocks. S-blocks are always aligned in g-blocks. Other blocks form i-blocks.
- Speed up SplitRepeats. Improve time complexity by building the tree from diagnostic positions. Critical for blocks of > 500 fragments.
- PostProcessing produces new files:
- table of global blocks' properties (
- blockset alignments with block names (
- table of global blocks' properties (
- Mutations file parser written in Python (example)
- Print local time with timezone offset to logs
- Add descriptions of some algorithms (
- Translate ECCB'14 abstract into Russian
- Fix bugs:
- Fix bugs in GUI
- Fix bugs in annotations parser (GetData)
- Fix bugs in local blockset alignment builder. It used to consider linear sequences to be circular.
- Change alignment requirements. Require high similarity in every slice of length
Version 0.3.1. Bug fix.
- fix crashing in processor MergeUnique.
Version 0.3.0. Improvements.
- non-compatibles changes of formats,
- new syntax of of script language added (see API.md),
- Fragment now has not
- some processors were renamed,
- documentation was updated and improved,
- Windows 64bit build,
- LuaJIT by default,
- blockset alignment is build in global blocks,
- GUI: search by sequence.
Version 0.2.5. Cleanup, bugfix:
- fix MergeUnique fail if sequence has only 2 fragment,
- fix MakePangenome's imperfections on joining,
- prevent BLAST failures on long N's (split before blasting),
- move FragmentCollection to model/,
- add new features to FragmentCollection,
- fix bug in FragmentCollection.remove,
- start moving code from fragment.prev/next to FragmentCollection (Rest, Joiner, bsa, MergeUnique),
- remove FragmentDiff, fragment.split, fragment.exclude, fragment.shift, OneByOne,
Sequence.circular()doesn't throw (linear by default),
Sequence.set_name()throws if name includes space or underscore,
- fix memory leak in a test.
Version 0.2.1. Bugfix:
- Windows Uninstaller removes all shortcuts from Start,
- mycoplasma example,
- fix app path discovery if UPX'ed,
- wrap cmd with quotes if it contains spaces,
- BlastFinder: do not crash if input is empty,
- GetData can copy specific records from local files.
Version 0.2.0. Cleanup:
- TrySmth: fix error (subblocks),
- Pangenome: make sure result blocks can not be joined,
- remove deprecated and unused code and options,
- change format of config files,
- read config
npge.conflocated in application dir,
- group options to sections and hide some of them,
- change format of
genomes.tsv(no automagic, can read from file),
- import other features, not only genes, update GUI,
- GUI/search: not only wildcard search,
- GUI: ignore missing additional input files,
- print "Running...", ".. done",
- less technical output of Pangenome,
- rename :cin => :stdin, :cout => :stdout, :cerr => :stderr,
- remove filter options
Version 0.1.4. Bugfix:
- clarifications in README,
- fix parsing errors in
- fix possible test failure,
- fix possible terminal freeze,
- support alternative Lua implementation LuaJIT,
- Windows Wizard creates more shortcuts,
- throw exception on file openning error.
Version 0.1.3. Bugfix:
- configure to use blast plus for static build,
- add blast to requirements,
- move from hg and bitbucket to git, github,
- update npge.ico,
- one-line build commands.
Version 0.1.2. Bugfix:
- fix "Pangenome" (some blocks were not joined),
- fix freeze in
- do not use CURL,
- fix many build issues,
- all-steps.sh for Windows and Linux,
- run tests before packaging,
- fix all tests to run them from wine,
- Linux static build + package.
Version 0.1.1. Bugfix:
- fix running MergeUnique in Pangenome,
- MergeUnique's crash on unique fragments located between two fragments of one block was fixed,
- fixed several bugs when search in GUI by sequence, containing 'N's,
- add icon npge.ico, use it in GUI,
- Processor memorizes global Meta in its consctuctor,
- fix Lua function arg_value,
- Stem is now exact in Info,
- NEWICK representation of trees is now multiline,
- set default number of threads to number of cores,
- windows: build.sh uses current source dir,
- windows: script package.sh and Installation Wizard,
- typos in README fixed.
Version 0.1.0. Features developed in Summer 2014 were incorporated in ver. 0.1.0. It was published prior to ECCB'14 event.
Corresponding author: Boris Nagaev, email: firstname.lastname@example.org
Copyright (C) 2012-2016 Boris Nagaev