showTree can visualize the phylogeny, protein sequences and protein domains of a gene family in one figure.

A Java Swing application for producing pretty drawings of trees (i.e., acyclic connected graphs).

2020. Визуализация алгоритмов для деревьев (произвольного дерева, двоичной кучи, красно-черного дерева, би-дерева; WebGL, threeJS, 3d-force-graph; React, Material-UI).

No description available

Need your feedback on the following things for PICS & ChIPsim installation . The following error I am getting: > source("http://bioconductor.org/biocLite.R") Bioconductor version 3.1 (BiocInstaller 1.18.2), ?biocLite for help > biocLite("PICS") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.1 (BiocInstaller 1.18.2), R version 3.2.0. Installing package(s) 'PICS' also installing the dependencies 'GenomeInfoDb', 'XVector', 'Biostrings', 'BiocParallel', 'BiocGenerics', 'IRanges', 'GenomicRanges', 'Rsamtools', 'GenomicAlignments', 'S4Vectors' trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/GenomeInfoDb_1.4.0.tar.gz' Content type 'application/x-gzip' length 272984 bytes (266 KB) ================================================== downloaded 266 KB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/XVector_0.8.0.tar.gz' Content type 'application/x-gzip' length 53480 bytes (52 KB) ================================================== downloaded 52 KB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/Biostrings_2.36.1.tar.gz' Content type 'application/x-gzip' length 12733397 bytes (12.1 MB) ================================================== downloaded 12.1 MB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocParallel_1.2.2.tar.gz' Content type 'application/x-gzip' length 428595 bytes (418 KB) ================================================== downloaded 418 KB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/BiocGenerics_0.14.0.tar.gz' Content type 'application/x-gzip' length 36236 bytes (35 KB) ================================================== downloaded 35 KB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/IRanges_2.2.1.tar.gz' Content type 'application/x-gzip' length 545148 bytes (532 KB) ================================================== downloaded 532 KB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/GenomicRanges_1.20.3.tar.gz' Content type 'application/x-gzip' length 910901 bytes (889 KB) ================================================== downloaded 889 KB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/Rsamtools_1.20.2.tar.gz' Content type 'application/x-gzip' length 2977142 bytes (2.8 MB) ================================================== downloaded 2.8 MB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/GenomicAlignments_1.4.1.tar.gz' Content type 'application/x-gzip' length 1944615 bytes (1.9 MB) ================================================== downloaded 1.9 MB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/S4Vectors_0.6.0.tar.gz' Content type 'application/x-gzip' length 184195 bytes (179 KB) ================================================== downloaded 179 KB trying URL 'http://bioconductor.org/packages/3.1/bioc/src/contrib/PICS_2.12.0.tar.gz' Content type 'application/x-gzip' length 828432 bytes (809 KB) ================================================== downloaded 809 KB * installing *source* package 'BiocParallel' ... ** R ** inst ** preparing package for lazy loading Error in namespaceExport(ns, exports) : undefined exports: walkCode, makeCodeWalker, showTree, makeConstantFolder, constantFold, isConstantValue, getAssignedVar, makeLocalsCollector, collectLocals, findLocals, findLocalsList, findFuncLocals, flattenAssignment, makeUsageCollector, collectUsage, findGlobals, checkUsage, checkUsageEnv, checkUsagePackage Error : unable to load R code in package 'BiocParallel' ERROR: lazy loading failed for package 'BiocParallel' * removing '/Apps/R/R-3.2.0/lib64/R/library/BiocParallel' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/BiocParallel' * installing *source* package 'BiocGenerics' ... ** R ** inst ** preparing package for lazy loading Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/Apps/R/R-3.2.0/lib64/R/library/parallel/libs/parallel.so': /Apps/R/R-3.2.0/lib64/R/library/parallel/libs/parallel.so: undefined symbol: __sched_cpucount Error : package 'parallel' could not be loaded ERROR: lazy loading failed for package 'BiocGenerics' * removing '/Apps/R/R-3.2.0/lib64/R/library/BiocGenerics' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/BiocGenerics' * installing *source* package 'S4Vectors' ... ** libs gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c AEbufs.c -o AEbufs.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c DataFrame_class.c -o DataFrame_class.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Hits_class.c -o Hits_class.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c List_class.c -o List_class.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_class.c -o Rle_class.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Rle_utils.c -o Rle_utils.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SEXP_utils.c -o SEXP_utils.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c SimpleList_class.c -o SimpleList_class.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c anyMissing.c -o anyMissing.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c eval_utils.c -o eval_utils.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c hash_utils.c -o hash_utils.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c int_utils.c -o int_utils.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c logical_utils.c -o logical_utils.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c safe_arithm.c -o safe_arithm.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c sort_utils.c -o sort_utils.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c str_utils.c -o str_utils.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c subsetting_internals.c -o subsetting_internals.o gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c vector_utils.c -o vector_utils.o gcc -std=gnu99 -shared -L/usr/local/lib64 -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o eval_utils.o hash_utils.o int_utils.o logical_utils.o safe_arithm.o sort_utils.o str_utils.o subsetting_internals.o vector_utils.o installing to /Apps/R/R-3.2.0/lib64/R/library/S4Vectors/libs ** R ** inst ** preparing package for lazy loading Error : package 'BiocGenerics' required by 'S4Vectors' could not be found ERROR: lazy loading failed for package 'S4Vectors' * removing '/Apps/R/R-3.2.0/lib64/R/library/S4Vectors' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/S4Vectors' * installing *source* package 'IRanges' ... ** libs gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/Apps/R/R-3.2.0/lib64/R/library/S4Vectors/include" -fpic -g -O2 -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o In file included from IRanges.h:1, from CompressedIRangesList_class.c:4: ../inst/include/IRanges_defines.h:18:31: error: S4Vectors_defines.h: No such file or directory In file included from CompressedIRangesList_class.c:4: IRanges.h:104: warning: type defaults to 'int' in declaration of 'IntPairAE' IRanges.h:104: error: expected ';', ',' or ')' before '*' token IRanges.h:109: warning: type defaults to 'int' in declaration of 'IntPairAEAE' IRanges.h:109: error: expected ';', ',' or ')' before '*' token IRanges.h:206: error: expected '=', ',', ';', 'asm' or '__attribute__' before '_get_elt_from_CompressedIntsList_holder' CompressedIRangesList_class.c:5:33: error: S4Vectors_interface.h: No such file or directory CompressedIRangesList_class.c: In function '_hold_CompressedIRangesList': CompressedIRangesList_class.c:21: warning: implicit declaration of function 'get_classname' CompressedIRangesList_class.c:21: warning: assignment makes pointer from integer without a cast make: *** [CompressedIRangesList_class.o] Error 1 ERROR: compilation failed for package 'IRanges' * removing '/Apps/R/R-3.2.0/lib64/R/library/IRanges' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/IRanges' * installing *source* package 'GenomeInfoDb' ... ** R ** inst ** preparing package for lazy loading Error : package 'BiocGenerics' required by 'GenomeInfoDb' could not be found ERROR: lazy loading failed for package 'GenomeInfoDb' * removing '/Apps/R/R-3.2.0/lib64/R/library/GenomeInfoDb' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/GenomeInfoDb' * installing *source* package 'XVector' ... ** libs gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/Apps/R/R-3.2.0/lib64/R/library/S4Vectors/include" -I"/Apps/R/R-3.2.0/lib64/R/library/IRanges/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o IRanges_stubs.c:1:28: error: _IRanges_stubs.c: No such file or directory make: *** [IRanges_stubs.o] Error 1 ERROR: compilation failed for package 'XVector' * removing '/Apps/R/R-3.2.0/lib64/R/library/XVector' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/XVector' * installing *source* package 'Biostrings' ... ** libs Warning in gzfile(file, "rb") : cannot open compressed file '/Apps/R/R-3.2.0/lib64/R/library/S4Vectors/Meta/package.rds', probable reason 'No such file or directory' Error in gzfile(file, "rb") : cannot open the connection * removing '/Apps/R/R-3.2.0/lib64/R/library/Biostrings' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/Biostrings' * installing *source* package 'GenomicRanges' ... ** libs gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/Apps/R/R-3.2.0/lib64/R/library/S4Vectors/include" -I"/Apps/R/R-3.2.0/lib64/R/library/IRanges/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o IRanges_stubs.c:1:28: error: _IRanges_stubs.c: No such file or directory make: *** [IRanges_stubs.o] Error 1 ERROR: compilation failed for package 'GenomicRanges' * removing '/Apps/R/R-3.2.0/lib64/R/library/GenomicRanges' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/GenomicRanges' * installing *source* package 'Rsamtools' ... ** libs gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/Apps/R/R-3.2.0/lib64/R/library/S4Vectors/include" -I"/Apps/R/R-3.2.0/lib64/R/library/IRanges/include" -I"/Apps/R/R-3.2.0/lib64/R/library/XVector/include" -I"/Apps/R/R-3.2.0/lib64/R/library/Biostrings/include" -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -Dfprintf=_samtools_fprintf -Dexit=_samtools_exit -Dabort=_samtools_abort -I./samtools -I./samtools/bcftools -I./tabix -fpic -g -O2 -c Biostrings_stubs.c -o Biostrings_stubs.o Biostrings_stubs.c:1:31: error: _Biostrings_stubs.c: No such file or directory make: *** [Biostrings_stubs.o] Error 1 ERROR: compilation failed for package 'Rsamtools' * removing '/Apps/R/R-3.2.0/lib64/R/library/Rsamtools' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/Rsamtools' * installing *source* package 'GenomicAlignments' ... ** libs gcc -std=gnu99 -I/Apps/R/R-3.2.0/lib64/R/include -DNDEBUG -I/usr/local/include -I"/Apps/R/R-3.2.0/lib64/R/library/S4Vectors/include" -I"/Apps/R/R-3.2.0/lib64/R/library/IRanges/include" -fpic -g -O2 -c IRanges_stubs.c -o IRanges_stubs.o IRanges_stubs.c:1:28: error: _IRanges_stubs.c: No such file or directory make: *** [IRanges_stubs.o] Error 1 ERROR: compilation failed for package 'GenomicAlignments' * removing '/Apps/R/R-3.2.0/lib64/R/library/GenomicAlignments' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/GenomicAlignments' * installing *source* package 'PICS' ... checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for GSL... no checking for gcc... gcc -std=gnu99 checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc -std=gnu99 accepts -g... yes checking for gcc -std=gnu99 option to accept ISO C89... none needed checking for gsl-config... /usr/local/bin/gsl-config checking for GSL - version >= 1.6... no *** Could not run GSL test program, checking why... *** The test program compiled, but did not run. This usually means *** that the run-time linker is not finding GSL or finding the wrong *** version of GSL. If it is not finding GSL, you'll need to set your *** LD_LIBRARY_PATH environment variable, or edit /etc/ld.so.conf to point *** to the installed location Also, make sure you have run ldconfig if that *** is required on your system *** *** If you have an old version installed, it is best to remove it, although *** you may also be able to get things to work by modifying LD_LIBRARY_PATH configure: error: Cannot find Gnu Scientific Library >=1.6 ERROR: configuration failed for package 'PICS' * removing '/Apps/R/R-3.2.0/lib64/R/library/PICS' * restoring previous '/Apps/R/R-3.2.0/lib64/R/library/PICS' The downloaded source packages are in '/tmp/Rtmp1HbCZE/downloaded_packages' Updating HTML index of packages in '.Library' Making 'packages.html' ... done There were 11 warnings (use warnings() to see them)

Sample Code from weka to show tree j48

ShowTree: A Shell Script for Displaying Folder Structure with Color-Coding and Advanced Formatting Options

No description available

A file utility command

solution of 'showtree'

when you click element ,show the elemement and you can add some attr on it

No description available

No description available

No description available

No description available

Bash script allowing the user to show their current repository tree with more options (color of file types, icons, image preview, tree level)

Print tree structures

Show-TreeWithDates is a PowerShell function that generates a directory tree similar to the tree command, including the last modified date and time for each file and folder. It’s useful for audits, file inspections, or quick structure overviews on Windows, supporting recursive depth control, console output, and file export.

Linux...

No description available

No description available

No description available

No description available

ESP8266 ShowTree 196L c6 RGB(built-in 6011)

No description available