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10 apr 2013 · A new way to write lyrics. RapPad combines a bunch of language tools that help you analyze and write lyrics like never before. There is a built-in rhyming dictionary, syllable counter, thesaurus, line generator, and much more. You can also attach an instrumental or recording to your lyrics and control it from the same interface.
However, this technique alone may not keep you entirely on track, so it can be used in combination with another known as ‘RAPPAS’. This translates as: Relevant – The skill you put forward needs to be relevant to what is being asked for.
Animated Films Produced or Directed by Panagiotis Rappas
- Overview
- RAPPAS
- Description
- Installation
- Usage
- License
•This repository is hardly maintained anymore.
•Devolpments moved to C++.
•The second iteration of the approach is renamed EPIK.
•It is order(s) of magnitude faster, and requires order(s) of magnitude less RAM.
Repository: EPIK repository
Improvements compared to RAPPAS : https://doi.org/10.1093/bioinformatics/btad692
•Documents: Usage, Tutorial and Benchmarking
•Please cite:
Rapid Alignment-free Phylogenetic Placement via Ancestral Sequences
Benjamin Linard, Krister Swenson, Fabio Pardi.
Bioinformatics, Volume 35, Issue 18, 15 September 2019, Pages 3303–3312
doi.org/10.1093/bioinformatics/btz068
RAPPAS (Rapid Alignment-free Phylogenetic PLacement via Ancestral Sequences) is a program dedicated to "Phylogenetic Placement" (PP) of metagenomic reads on a reference tree. As apposed to previous PP programs, RAPPAS is based on the phylo-kmers idea, detailed in tis manuscript and uses a 2 step approach divided into a) the database build, and b) the placement itself.
The main advantage of RAPPAS is that it is alignment free, which means that after step (a) (the DB build) is performed, metagenomic reads can be directly placed on a referene tree WITHOUT aligning them to the reference alignment on which the tree was built (as required by other approaches).
The second advantage of RAPPAS is its algorithm based on phylo-kmers matches, making its execution time linear with respect to the length of the placed sequences.
RAPPAS was funded from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 634650. (Virogenesis.eu)
Bioconda installation
If you use bioconda, you can install RAPPAS with the following commands: Then you can run RAPPAS with the command: If you need to customize Java JVM parameters (for instance when requesting more memory with options -Xmx/-Xms), use the following bash command:
From sources: prerequisites
•RAPPAS compilation requires a clean javac compiler installation. Java >=1.8 is compulsory as some operations are based on Lambda expressions. •Apache Ant is used to facilitate the compilation. We provide instructions for Debian-based Linux distributions. For compiling Java sources with Apache Ant on other operating systems, please perform analogous operations on your system. Using OpenJDK 1.8 (more recent versions also compatible): Using the proprietary Oracle JDK 1.8 (more recent versions also compatible): Installation of Apache Ant:
From sources: download and compilation
The executable RAPPAS.jar can then be found in the ./dist directory. You can create also create a standalone executable using a stub. If you use this approach, be aware you will need to setup the java virtual machine options manually by modify the stub.sh file and that they cannot be modified later. When using the standalone binary and not the jar file, in all instructions and tutorials just remember to replace 'java [jvm_options] -jar RAPPAS.jar' by 'rappas' in the instructions and tutorials detailed below.
Reference Dataset
First, one has to prepare a reference dataset designed to answer a biological question. Typically, in the context of metagenomics and taxonomic identifications, a marker gene (16S rRNA, cox1, rbcl...) is used to build a reference species tree. This species tree is the basis for phylogenetic placement of marker gene(s). For RAPPAS, the reference dataset is composed of: 1.A reference alignment of all sequences of this marker gene 2.A phylogenetic tree inferred from this reference alignment Such reference marker gene datasets can be found, for instance from: •"The All-Species Living Tree" Project (LTP, eukaryote rRNAs) : https://www.arb-silva.de/projects/living-tree/, •Greengenes (bacterial 16S) : http://greengenes.secondgenome.com/, •Any marker database from EukRef: http://eukref.org/databases/, •The curated database of Eukref : http://eukref.org/databases/, •Or built internally in the lab.
Sharing pre-built RAPPAS databases
While our goal is to allow stable databases that can be broadly shared, RAPPAS is still in active development. Some major changes may induce that a recent version (ex: v1.05) becomes incompatible with a DB built using an older version (ex: v1.01). Such incompatibilities are clearly stated in the "release" page and the changelog. Also be aware that, because uses internal Java serialization, you may run to troubles when sharing databases between users using different Java versions or Oracle JDK VS OpenJDK.
RAPPAS database build
Basic command where Note on PhyML, PAML and RAxML binaries: Currently, the following programs are fully supported by RAPPAS for generating ancestral sequence posterior probabilities: •RAxML-ng : Fastest & recommended but may require lots of RAM (you have to use phyml-v3.3.20180214). •PhyML : ~10x slower, requires slightly less memory. •PAML : ~100x slower, but very low memory footprint. Note on -Xm[x]G option: The process of database build can be memory intensive for values of k>=10. To make RAPPAS run smoothly, allocate more memory (more heap) to the java process using the option -Xm[x]G where [x] is replaced by an integer value. For instance, -Xm8G will extend the java heap to a maximum of 8Gb of memory, -Xmx16G will extend it to a maximum of 16Gb ... You can use the latest versions provided on the authors' websites. PhyML requires at least version 3.3 (see PhyML GIT ), but we recommand the HACKED VERSIONS available in this git repository in the /depbin directory. These are based on slightly modified sources of PhyML and PAML: no change in ML computations, but useless outputs are skipped, making the ancestral reconstruction process faster (in particular for PAML). The reconstruction will result in the production of a directory structure and a database file in the given "workdir":
RAPPAS is available under the GPLv3 license.
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Postdoctoral Research Fellow. 2009 - 2010. Alexis Rappas (PhD in History and Civilization, European University Institute, 2008) is an Assistant Professor in History at Koç University in Istanbul. His research focuses on European colonialism in post-Ottoman settings.
Rappas: Directed by Crystal Ellis. With Taetta Chip, Tyrell Ellis, Hakim Muhammad, Omar Mosley. Twins Gary and Cary are set on being big time rap singers (rappas), but the only problem is they don't have any talent! Desperate for big bucks and fame they are suckered into signing a bogus 30 album deal with Twitch Records.
