With Single Molecule, Real-Time (SMRT) Sequencing, you can access structural variations having a broad range of sizes, types, and GC content with the ability to:

• Uncover missing heritability linked to structural variation
• Unambiguously identify genomic context and variant breakpoints at the sequence level to unravel the genetic etiology of disease
• Resolve structural variation across the complete size spectrum with basepair resolution

Following are the SV tools, which can assist you to achieve your goal.

Sniffles: Structural variation caller using third generation sequencing

Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Please note the current version of Sniffles requires sorted output from BWA-MEM (use -M and -x parameter) or NGM-LR with the optional SAM attributes enabled! 

More at https://github.com/fritzsedlazeck/Sniffles

MultiBreak-SV: It identifies structural variants from next-generation paired end data, third-generation long read data, or data from a combination of sequencing platforms.

There are two pieces of software in this release: (1) a pre-processor that takes machineformat (.m5) BLASR files, and (2) MultiBreak-SV. For installation and usage instructions, see doc/MultiBreakSV-Manual.txt.

More at https://github.com/raphael-group/multibreak-sv

Parliament: A Structural Variation Tool. Why ask a single sv-detection approach to find every variant when you can have a parliament of tools deciding?

Publication about the algorithm and “…the first long-read characterization of structural variation in a diploid human personal genome…” (HS1011) - “Assessing structural variation in a personal genome—towards a human reference diploid genome”

More at https://sourceforge.net/projects/parliamentsv/

https://www.dnanexus.com/papers/Parliament_Info_Sheet.pdf

PBHoney: the structural variation discovery tool 

PBHoney is an implementation of two variant-identification approaches designed to exploit the high mappability of long reads (i.e., greater than 10,000 bp). PBHoney considers both intra-read discordance and soft-clipped tails of long reads to identify structural variants.

Read The Paper http://www.biomedcentral.com/1471-2105/15/180/abstract

More at https://sourceforge.net/projects/pb-jelly/

SMRT-SV: Structural variant and indel caller for PacBio reads

Structural variant (SV) and indel caller for PacBio reads based on methods from Chaisson et al. 2014.

SMRT-SV provides an official software package for tools described in Chaisson et al. 2014 and adds several key features including the following.

• Unified variant calling user interface with built-in cluster compute support
• Small indel calling (2-49 bp)
• Improved inversion calling (screenInversions)
• Quality metric for SV calls based on number of local assemblies supporting each call
• Higher sensitivity for SV calls using tiled local assemblies across the entire genome instead of "signature" regions
• Genotyping of SVs with Illumina paired-end reads from WGS samples

More at https://github.com/EichlerLab/pacbio_variant_caller

Orthology relations can be used to transfer annotations from one gene (or protein) to another. Hence, detecting orthology relations has become an important task in the post-genomic era. Various genomic events, such as duplication and horizontal gene transfer, can cause erroneous assignment of orthology relations. In closely-related species, gene neighborhood information can be used to resolve many ambiguities in orthology inference. Here we present OrthoGNC, a software for accurately predicting pairwise orthology relations based on gene neighborhood conservation. Analyses on simulated and real data reveal the high accuracy of OrthoGNC. In addition to orthology detection, OrthoGNC can be employed to investigate the conservation of genomic context among potential orthologs detected by other methods. OrthoGNC is freely available online at http://bs.ipm.ir/softwares/orthognc and http://tinyurl.com/orthoGNC.

http://www.comp.nus.edu.sg/~wongls/projects/orthoGNC/

Address of the bookmark: http://www.sciencedirect.com/science/article/pii/S1672022917301663

3D-Dock Suite

Global rigid search: FFTShape complementarity and electrostatics

Re-scoring and clustering. Refinement of interface side-chains

3D-Garden

Global rigid search in ensamble

Shape complementarity and Lennard–Jones potential

Side chain and backbone dihedral refinement

DOT

Global rigid search: FFTShape complementarity, electrostatics and VDWNone

Escher NG

Global rigid searchShape complementarity, hydrogen bonds and electrostatic

Integrated in VEGA

GRAMM 

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potential

Clustering of conformations

GRAMM-X 

Global rigid search: FFT. smooth protein surface representation for soft docking

Shape complementarity and Lennard-Jones potentialminimization and re-scoring with multiple filters

HEX

Global rigid search: Fourier correlation of spherical harmonics

Shape complementarity

HADDOCK

Global rigid searchElectrostatic ,VDW and desolvation energy termsMD simulated annealing refinement . Filtering based on external data. 

ICM

Global rigid search: Monte CarloEmpirical scoring function

Clustering and selection of conformations. Refinement of interface side-chains and re-scoring

MolFit 

Global rigid search: FFTShape complementarity

Clustering of good solutions, filtering using a priori information and small, local rigid rotations around selected conformations

PatchDock

Global rigid searchShape complementarity and atomic desolvation energy

Clustering of conformations

PyDock

Global rigid search:FFTShape complementarity

rescoring by binding electrostatics and desolvation energy

RosettaDock

Local rigid search: Monte Carlo with low and high resolution structure representation levels

Different scoring parameters for the different resolutions 

ZDOCK

Global rigid search: FFTShape complementarity, desolvation energy, and electrostatics.

Energy minimization and re-scoringFree for academics

Point to note:

The proper treatment of flexibility in protein–protein docking is still an active field of research. You first should analyzed your proteins in order to define their conformational space and then choose the most suitable method for your docking problem.

Address of the bookmark: http://www.bioapp.org/ewas/

Address of the bookmark: https://www.ezbiocloud.net/tools/orthoani

IQ-TREE found higher likelihoods between 62.2% and 87.1% of the studied alignments, thus efficiently exploring the tree-space. If we use the IQ-TREE stopping rule, RAxML and PhyML are faster in 75.7% and 47.1% of the DNA alignments and 42.2% and 100% of the protein alignments, respectively. However, the range of obtaining higher likelihoods with IQ-TREE improves to 73.3–97.1%. IQ-TREE is freely available at http://www.cibiv.at/software/iqtree

Address of the bookmark: http://www.iqtree.org/

• Homology-based misassembly correction
• Homology-based assembly scaffolding and patching
• Scaffold merging

Address of the bookmark: https://github.com/malonge/RagTag

Features

• Circular and linear views of genomes

• Capable of drawing genomes up to 10 Mbp with 1000's of features and 100's contigs

• Smooth zooming down to the sequence level

• Easily generate features and plots directly form the sequence (e.g. ORFs, GC-content and GC-Skew)

• Save high resolution PNG maps up to 8000x8000px

• Fully documented API for interacting with CGView.js maps

Address of the bookmark: https://js.cgview.ca/

Address of the bookmark: https://github.com/dentearl/evolverSimControl