Some considerations on this matter are found here:

https://www.researchgate.net/publication/235601668_Incorporating_molecular_data_in_fungal_systematics_a_guide_for_aspiringresearchers

Article Incorporating molecular data in fungal systematics: A guide ...

Thanks, but it wasn't as informative as I needed.

MrBayes can read binary data: 

http://mrbayes.sourceforge.net/wiki/index.php/Evolutionary_Models_Implemented_in_MrBayes_3#Restriction_Site_.28Binary.29_Model

and

http://treethinkers.org/wp-content/uploads/2013/05/MrBayes_tutorial_2013.pdf

However, first you should be sure that the alignment is correct. Second, maximum parsimony may be better criterion.

Anyway, indels must be coded first. If you are familiar with R and if you decide to use 5th state character or simple indel coding (recommended) methods,  consider using package haplotypes that I can help you:

http://cran.r-project.org/web/packages/haplotypes/index.html

Or you can use other software such as SeqState which supports a number of indel coding methods: 

http://bioinfweb.info/Software/SeqState

FastGap is a Windows executable program for fast and efficient assembly of DNA sequence alignment files. In the process, gap or indel characters can be coded and added to the data file as separate partitions:

http://www.aubot.dk/FastGap_home.htm

How I can use fastgap to concatenated its and lsu markers and use indel gaps as separate characters in phylogenetic analysis?

Alessandro Fellin , fastgap gives you as output a nexus block where sequences and indels are interleaved. If you add some commands, it is ready to be used in mrbayes. If you want your concatenated its-lsu-indel sequences in other formats, like fasta, I don't know any available program for conversion. Personally I use a python script very simple to do such operation.