There are a lot of such tools... for example, most of genome/transcriptome assembly tools don't have GUI. Among them are Velvet, SPAdes, SOAPdenovo etc. Associated software for NGS data processing, such as Trimmomatic also usually don't have GUI.

see under linux environment (debian or ubuntu)

Tools: bioperl and biopython, blast2, ncbi-blast + ncbi-epcr, rnahybrid, R ....

bioperl

Perl tools for computational molecular biology

http://www.bioperl.org/wiki/Main_Page

Python-biopython

Python library for bioinformatics

http://biopython.org/wiki/Main_Page

ncbi-blast +

next generation suite of BLAST sequence search tools

ncbi-epcr

Tool to test a DNA sequence for the presence of sequence tagged sites

rnahybrid

Fast and effective prediction of microRNA / target duplexes

R (r-bioc-genomifeatures)

GNU R tools for making and Manipulating transcript centric annotations

Matlab tools: (http://in.mathworks.com/products/matlab/)

Well I was looking for specific tools, not a package or library of a programming language. Like vina or modeller(I'm not sure it might have a gui developed by third party now).

Thanks anyway. 

There are a lot of such tools... for example, most of genome/transcriptome assembly tools don't have GUI. Among them are Velvet, SPAdes, SOAPdenovo etc. Associated software for NGS data processing, such as Trimmomatic also usually don't have GUI.

Rapidminer

https://rapidminer.com