so there not Borg do the same thing but i guess they put Machine in to organisms. When "The Beast" puts organisms in to machines right?
the borg us nano probes to create machines or implants inside a living host. The Beats are the opposite yes... they Infect a ship and create Bio matter that links all of it together. We have only esstablished that the Beast can attack from a distance where as the Borg must transfer on contact. Also borg nano probes are useless againest the beast infestation.
suggest you should implement a automatic self-destruct protocol for all ships. we the confederation did this a long time ago just in case the plague should its ugly face again. we just destroyed the Luna and the Texas it may have not saved the crew but it stopped the beast form growing.
That's the problem... the beast already know about auto distruct and can disable it easier than your command codes can incrypt it. once disabled they can use it to send a shockwave of Beast patricals into space and infect the ships it comes in contact with. They even learned how to turn Civilians and humaniods into Bio-warheads like the auto-distruct bombs.
Another probelm is when taking over a ship the Beast also Distroy the computer core and all energy banks. they use their own self suppied energy and their own Technology instead of the preset stuff. they will control defences and weapons but they will leave the life support and main computer without power... they are the ultimate invation force to be honest.
it would help if you had an image of this of what we are looking for
I can get you a picture of what the original beast look like. Images of the ships they infected shoulding be too hard to find. keep in mind most these images where taken during combat.

The Bentusi Exchange (Bentusi Motherships)
This is one of the more deadly ships in their fleet. Though the Beast have not been able to Replicate this ships desgin and complexity they don't hesetate to use it. Beware! They are fast, Powerful, Infectious and Extemely hard to destroy. also serves as Constuction vessel aswell as combat.

Any ship, Just unnatural grow.It's main perpouse is mothership. Heart of all combat. It can be made from any capital ship. It serves as main production, all Beast Fleets that are built are made at 1 of these. If you haven't guessed this ship is the most heavly Guarded in the Beast fleet. I expect you'll need A large army to conquer these.
Unfortunately the new and old beast use these ships, so only way to tell if their New or old is by the fleets that protect it. Not very fast, Powerful, The Most infectious Ship in the beast fleet and Regenerates it's hull for defence.

Infected fighters (Ships shown here are: Higarian Cloak Fighter{left}, Taidan Bomber{right})
Fighters are not normally feared in combat. But Beast fighters often are traveling with missiles, Bio-warhead. The Beast motherships can pump out about 35 of these a day serperately. They do not fire infectious Beams like that other vessels. they are too small to support much except the Beast itself. They us the fighter conventional weapon in combat. Though they are infectious if they decide to do a kamakazi run. Very fast, Not very powerful, not very infectious, Has little defence except speed.

Taidan Heavy Cruiser (Under attack, may not see it clearly)
This is the second most dealy ship. Taidan heavy cruisers are fairly easy for the beast to replicate, it just takes time. you can be sure they are in the lead of every fleet battle. Every since mothership has at the very least 4 cruisers guarding them. Aproach with care, they like to fire an infection beam to begin with. them will destory everything else with conventional weapons till the Beam recharges. Not very fast, Powerful, highly Infectious, The Taidan cruiser was made to take out a fleet single handly. It's got thick hull, backed with braces and energy shields. this plus anti-fighter cannons, which the beast use to relfect most weapons fire aswell.

Bio-warheads
In every fleet there are at least 30 of these missiles. they are easily made. a mothership can make about 50 each day. Beware! it only takes 2 to infest a large/medium class vessel, 1 small/tiny vessel, 3 Huge vessel. Very Fast, No weapons, Highly infectious, Radiation shielding.